humburg2,
Because of the many problems you are having I would either send your DCS unit back to MTH for a full up Grade, or talk to Barry and his crew about helping with the total up grade.
Further it sounds like you are trying to retro-fit your layout. Once your DCS is in the most current revision, I would go slow testing each part of the layout as I reto-fittered for DCS. Definitely use the programming track for programming your engines.
Make sure you safe guard your TIU with Scott 10 Amp breakers, if you are using old ZW & KW transformers to power your layout. Purchase Barry's DCS Companion Vol 2 and the OGR Video guide to DCS both, and us them as you retro-fit your layout. Get rid of the Atlas HD selector, until after you have fully proven out your DCS/TMCC controlled layout.
PCRR/Dave