Cory,
Cross part association is far from elementary.
I, like you have found it to be very ackward and confusing. I am sure that my lack of understanding is due to just that.
Consequently, I do not use it. Every once in a while I "play" with it in hopes of broadining my understanding.
I believe there are some tutorials that Sean has put together that you might try.
http://www.sdotson.com/index.asp
In the meantime you might just to want to turn it off.
Tools>Application Options>Assembly, and un-check the "Enable Associative Edge/Loop/Geometry Projection During in Place Modeling".
If you want CPA then hold down "Ctrl" when creating new geometry.
Regards,
Don A 🙂