If your track is wired through a 4PDT toggle switch, only the "RUN" position's polarity should be a concern. When you enter the "Program on a Program Track" function on your NCE system all track power is cut off and only the program track will be connected. But for "main line" programming on that same piece of track, proper polarity is essential.
It IS an operational siding connected up with a 4PDT toggle switch as per DCCWiki.
73
Bruce in the Peg
Only if your programming track is going to be a siding connected through a toggle switch so you can also run trains onto or off of it. If the programming track is totally isolated from the rest of the layout and cannot be used as an operational siding, then it doesn't matter because it will have power applied only when actually programming a decoder.
I don't know how you could check that, but the answer is "no".
Wiring my layout for the NCE system and I am keeping all outside rails connected to the same side of the command station output. I do this to maintain the correct phasing of the DCC signals.
My question is, do I need to maintain the same phasing for the program track output?