From the technical specifications for connecting the NCE Auto Switch, you may be able to get by with wiring both outputs to the same section of track and use it for both programming and operating, provided you're using a totally separate piece of track that is not a permanent part of your layout. The key to being able to do this is whether the Auto Switch has a neutral position between the two states so power is not applied to both outputs at the same time.
Information about the Auto Switch is very sketchy on the NCE web site other than the fact that it contains a mechanical relay to replace the normal DPDT toggle switch that many people use to switch a section of track between PROGRAM and OPERATE modes. What they don't say is whether the program track can be used as part of a main line when not in the program mode.
Your question should probably be addressed to NCE, but they are terrible about not answering e-mail.
Bruce Petrarca at Litchfield Station has been a lot more helpful and responsive than NCE.
There's also an NCE User's Group on Yahoo, but you have to be a registered member to use it.
I already have DPDT center-off toggle switches on programming track sections of my HO scale home layout and on our HO scale club layout, and know that these work very well because we can easily switch between the two modes and use a piece of mainline track for programming with an NCE PowerHouse Pro.
The only disadvantage to both the Auto Switch and the DPDT toggle is that the PowerHouse Pro shuts down the layout during programming sessions.
Here is the set up, Power Cab + Auto Sw + A piece of flex track to act as a programming track. The flex track is not connected in any way to the layout.
If I program say an address on the programming track, once I exit programming mode, will the Auto Sw let me run the engine on this same piece of flex track, just the same a if I move it to the layout?
I don't have a Auto Sw yet so I can't test that now.
Thanks
Jack W.