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The TSU-AT1000 is the Atlas style light board. It's thin and is usually an easy replacement for most light boards.
The TSU-1000 is the universal one. It comes with a harness that terminates with wires, but you can take the harness off and use the 9-pin socket (where the harness once was) to plug into an Athearn locomotive. Alternatively, you can get a harness for it that terminates with an 8-pin plug to plug into most DCC-ready locomotives.
The TSU-1000 takes up more room due to the thickness of the decoder and the 9-pin JST socket. You also have to take into account the thickness of the original light board that your TSU-1000 is plugging into.
Thanks for all the replies. I have ordered a Zephyr Xtra and now have to equip all of my locos for DCC. Do you have any recommendations on what you would put into Athearn Genesis SD 70, SD 70MAC, and the Athearn P42 Phase V locos? Thanks!!
For the SD70 series, I would get the Soundtraxx Tsunami TSU-1000 for the SD70ACe (the SD70 series has a specific start-up sound and the engine sounds on the SD70ACe sound better in general). In normal circumstances, I would use a TSU-AT1000 or a GN1000, but the SD70ACe soundset is currently only available for the TSU-1000.
For a P42, no one makes a dead on match for it, but you can get a Soundtraxx Tsunami TSU-AT1000 (the TSU-1000 will probably fit as well) for the GE FDL-16 prime mover and it will be close enough.