Well Bruce, as it happens, the confusion is all my fault (not for the first time). 
It's been many years since I did this last, and I left out the vital first step, sorry. To start with you do need to separate the decoders' rail pickup wiring so you can set their separate short addresses and identical long addresses individually on the Programming Track.
Once you have done that, they can be wired together and installed. Then you can do all your subsequent programming on the Main with your throttle or ideally JMRI DecoderPro, by changing CV29 back and forth as I outlined above.
I hope I didn't ruin your day. 
Pete
