Thanks for the replies. I'll get back to the model soon and keep going with:
1) the first floor generating the foundation
2) modifying the 1st floor until the auto generated foundation walls are the exact dimension
3) turning off auto-regenerate and manually add the rest of the walls to the foundation
4) set the foundation characteristics room by room
What does anybody think about the garage walls? It is block and could be generated in the foundation level. This would mean having a doorway from the garage (foundation level) into the mudroom (1st floor). On one hand it makes sense since the garage is block. On the other I could see how it would mess up the programs auto-configurator logic. Also, a roof would be placed directly on foundation walls. As opposed to spending a lot of time running down the wrong path... I will go with the normal method, but I was wondering if anyone had tried it before?