Commons
My personal preference here is the Direct Home Wiring or Two Wire System both rails isolated. Connect this common to a earth ground. This allows a common that is always at 0 volts and all other voltages at some + value above it. With no possible way for voltages to add or double. And use auto-reversing booster as you like or need.
It has been generally agreed upon in the DCC community, that common return should not be used with auto-reversing booster. The reasoning is that the normal practice for common rail at reverse sections is to place the common before the reversing mechanism, such as a switch, aux. contacts, modules, ect.  To do other wise can result in the adding of the two sources together. This is what happens when the common is connected the booster output, and the booster is reversed phase. The resulting doubling of the voltage can result in a damaged decoder. But there is more to it then this. It has always been there, it is nothing new with command control DCC or otherwise.
For drawings, explanations and other links as to how they all work look here. Commons & Reversing

Booster Phasing
If you have a problem with your Digitrax system with multiple boosters, that you get a short when a loco crosses over the gaps between booster districts. Or are adding your second booster to a Chief system, you might want to check this out.
After you get it all wired up and ready to go.. Before you run any locos.  Take throttle and select address 0, DC pulse stretched.. With no non decoder equipped locos on the layout turn the throttle way up..
Normally the track status light on the DCS100 and DB100s are yellow, AC signal on the track.. But when there is stretched pulses on the track, they will go either green or red pending polarity. The point here is to look at all your boosters and make sure they are all the same red or green on the track status light. If they are, then you have the phasing of the LocoNet cables going from booster to booster correct. If not just change the cable or replace the end with the proper connection.. 

Power Supplies
Just got your DCC system all hooked up. You have started running with your first loco and everything is fine. Now you add your second loco and seems like the locos all slowed down. Chances are you do not have a large enough power supply. The aux. or AC outputs of a DC power pack are not large enough to run you DCC system. Check with your manual or manufacturer of your system, find the min. power required for your system. This will be something like 18vac at 3-6 amps.

PR-1 Power Supply
If you have a PR-1 from Digitrax and are having problems reading decoder CVs, but it seems to write just fine. You more then likely do not have a proper power supply for it. First the supply must be well filtered, this means no AC ripple. Next the PR-1 will write over a wide range of voltages, but requires at least 15-18 vdc to read properly. More on the order of 16vdc to 18vdc to assure good readability. If the AC ripple is to high, you can add a 1000uf 35v Electrolytic Capacitor across the output of the power supply, be sure to observe polarity here.
For my PR-1 I use a Radio Shack adapter model #273-1652D 500mA at 12vdc. Yes it is a 12vdc supply, but as with most unregulated supplies, it puts out 17vdc no load.
Another useful supply is two 9 volt batteries wired in series. This will supply the required 18 Vdc, as pure as it comes, no filter required. And the PR1 draws very little current. These batteries will last a long time. And offers one more advantage, when the PR1 is used with a portable computer, this makes the PR1 totally portable.
A couple of hints from Dr Hans Tanner, the author of the PR-1 software:
Hint: If you use a RS232 interface with FIFO option make sure to switch off this option.
Hint: Standard baud rate for the PR-1 is 16,457 baud. Some older decoders as well as decoders from a few manufacturers program better if you use 19,200 baud. Please select the appropriate option in the port menu.

Still having problems getting the results desired from the PR1, check out the PR1 Help Page.

12-16 volts lamps use a 22-40 ohm resistor in series with the lamp.
3 volt 50 mA. lamps use a 330 ohm resistor in series with the lamp.
1.5 volt 50 mA. lamps use a 250 ohm resistor in series with the lamp.
1.5 volt 25 mA. lamps use a 560 ohm resistor in series with the lamp.
LED's  use a 680 ohm resistor in series with the LED.

All values are approx. and may need adjusted for your decoders and track voltage, but will make a good starting point. All resistors a 1/2 watt. Keep in mind higher Ohms values = dimmer lamps, and lower Ohms values = brighter lamps.

Understanding Ohm's Law  for larger scales and how to properly figure out the resistor value needed for a given lamp size.

Lighting Projects  for some simple schematics on how to install and wire lighting. As well as using voltage regulation for 1.5 volt lamps.

Static Build Up
Does it seem like you are loosing locos on your Digitrax system when you unplug a throttle and move to the next location and plug in.  This could be caused by static built up on the system. Did you catch the part in the Digitrax manual about grounding the ground connections to an earth ground. It not only good common safety, but also goes a long way to keep static from building up on the system.

Decoder Installs with NMRA plugs
If your loco has the NMRA plug, this makes a decoder install easy. All you need to do is find room for the decoder and plug in the decoder. Before you do, I would recommend you check out the socket on the loco first. You need to make sure there are no shorts from any pin to any other pin. If there is it needs to be corrected. This might be caused by a solder bridge on the underside of the PC board, a shorted diode, a stray wire connected to the PC board, ect.  Use a Ohm meter and check all pins against the others. You are looking for dead shorts. You might find resistance due to diodes, resistors, lamps, etc. But any dead shorts need to be corrected.
Any dead short can result in the loss of a function in the decoder, or worse the loss of the decoder.

Testing Decoder Installs
You have just finished installing a decoder in that new loco and are really ready to see it run.. STOP! The first place that loco should go is a current limited programming track, such as the service mode track, PR1, ect. I know you were really careful and followed the directions, double checked everything. But we are all human and make mistakes. The protection offered by the programming track, might just catch it for you and give you a chance to correct it. If there does happen to be a mistake or short, the power from the operations rails will more then likely not let you have a chance to correct it..

Who is Buzzing
Ah your DCC system supports analog DC locos. But the first thing you notice is when that loco is on the rails and just sitting there it buzzes. This is normal and is due to the nature of the DCC power on the rails.. With DCC the signal is the power, neat. The power on the rails is a bi-polar AC square wave form. This means it's polarity is changing back and forth at the DCC frequency. We all know what happens when we reverse the polarity of our DC power packs, the loco goes the other way. Now think what will happen if we could switch the direction switch back and forth on a DC power pack something like 10 thousand times a second. I know you can't do it, and even if you could the switch would not take it very long. But if you could, the loco would start to buzz, because it is trying to change direction at that same frequency. This will also cause the motor to heat up some. Is this hard on the motor, while there does seem to be a little debate on this. But as a rule of thumb, as long as the amplitude of the DCC signal does not exceed the stall rating of the motor, you should be ok. But it is still a good idea not to leave a DC loco sitting around idling on the rails. Once the loco starts to move the buzzing will stop.
Most open frame and can motors should be ok.
But Never use a DC coreless motor without a decoder on a DCC system!

Fuses
This is a very important safety issue. If you decide to build your own power supply for you DCC system. Make sure you follow any directions that the manufacturer of your system provides. Also make sure you fuse both the secondary [low voltage] and primary [high voltage] sides of the transformer/s. This is very important here. If you just fuse the secondary, this will protect the transformer from over heating from any excessive load on it from the system. If you just fuse the primary, this will protect from a fire caused by a shorted transformer. But as you can see, I hope, you need both sides fused to be protected.
Now comes the problem, what size fuses to use. Well the secondary side is easy, you know what the max. output of your booster is and the max. rating of the transformer, find the lower of the two, so the fuse should come close to matching that. Again check your manuals or check with the system manufacturer. But how do you know or find the primary fuse side. Well actually it is really not hard at all. At least if you know a little about Ohms Law and even if you do not the formula is very easy to figure.
The first thing you need to know is the power of the secondary side, this is called Watts. To find the Watts, just multiply the volts times the amps.  ex: With a 18vac secondary at 6 amps, and a 5 amp booster, the booster would be the lower,  this would be 90 watts. So now all we have to do is reverse the math using the primary side voltage. ex: 120 vac divided in to 90 watts would equal 0.75 amps a 1 amp slow blow fuse would be a good choice here. And a 5 amp fuse for the secondary.
Again, this is a safety issue so if you do not understand this, then find someone who does, or by a commercial DCC power supply.

Coreless Motor
Another debatable issue are coreless motors safe on a DCC system. Never on DCC without a decoder! But once a decoder is installed the debate starts. I personally have two locos with coreless motors in them. They have not only survived the old DC days, the analog CC days, they are still running fine on the DCC system. One thing to keep in mind is not all motors coreless or otherwise are created equal, they all have ratings. The best choice here is again talk it over with the system manufacturer about it. If you still are not sure, here is a hint from years ago.
Put a 3 to 6 volt ballast lamp inline with the motor and the decoder. The lamp will limit the amount of current that can be sent to the motor and also act as a shock absorber for the pulses. Finding the proper lamp will be a matter of trial and error to get the proper characteristics required.