Ahh, ok, that makes sense now. I was wondering why faces would be highlighted when mousing over features in the PathFinder. Part of my confusion stems from the Live Rules as well. I'm starting to get the hang of modifying the part using the steering wheel, but I can't seem to get the right modifications much of the time, probably because the live rules need to be changed.
For example, consider a truncated cone. If I wanted to extrude a cylindrical section from either end, how would I need to set the live rules? It currently wants to extrude with the taper of the base feature.