With all of these Atlas switches you say you installed, did you create a crossover or turn-around loop in your trackwork where the track makes a loop to go back the other way or crosses over from one side of hte layout to the other? If you did, that's the source of the short. In situations such as this you have to put insulated rail joiners in the track.
You need to seek out, download, and print a file called "Wiring for DCC" that is on one of these forums.
I was going to suggest that you get a voltmeter, but that won't really help unless you already understand what to look for.
Took all of the rolling stock, etc. off and the short remained. Created a new main by putting a couple of pieces of track together and it ran ok. When I attached this new main track to the existing layout it went dead. The only lines to the track are one set from the power pack to the Atlas connector track. I have added a lot of Atlas manual switches to the Atlas Flextrack and have looked at all of them but can see no problems. Is there some kind of tool? I can get that I can run over the track in the layout to see where a short might be? Thanks
Take all locomotives and rolling stock off the layout and see if the short goes away. If it doesn't, then the short is in your wiring. Maybe you have a set of track feeder wires crossed if you used more than one set. Disconnect feeder wires and then reconnect them one at a time. When the short returns, that set of feeder wires is reversed.
If it works OK when only connected to the separate program track, the unit is OK. Look for a short in your wiring or track. Place an ohmmeter across the two disconnected track leads to see if there is any resistance that would indicate a short circuit.
My Prodigy Advance won't run right. It indicates a short? Green lights flashing back and forth. Fan turns on briefly and then stops. Works ok when just connected to separate Program Track. Otherwise cannot get it to power engines, etc.. I've checked the track multiple times for shorts, etc.. None visible. Any ideas about what may be going on. It worked briefly and I ran an engine around. It lost power at a dead rerailer Atlas Code 100. Changed this. Had the engine go over another section on a curve and then it went dead. Can't see anything going on on this section of track. Used a volt meter and it shows that the track is capable of power. Trying to figure out how to possible isolate this or what else to consider. Thanks for any input.