Your post made me laugh - in a good way though. Yep, the EOS can "take over" as you put it, but that is no different to your digital bodies. Think of how you work with the digi bodies rather than the Bessas.
Don't know the rebel body (UK names were different) but the EOS 1's have custom functions to disable the auto ISO DX coding, disable the auto rewind, disable the auto leader retraction etc.
There must be an instruction manual online somewhere that can give all the CF fuctions and settings.
Btw, enjoy the camera!