I plan to change the focusing screen to let me use the manual focus lenses better. Changing the focusing screen shouldn't affect AF does it?
You will still be able to use AF, although some screens will mess with metering.
There are several options:
1. Do as you plan (I think?), and get a split screen focusing screen. I love using these on film SLRs, but they are not great for edge focus, and focus-recompose can lead to focus shifts, especially on FF (bear in mind, if you're using fast glass, stopping down can also lead to focus shifts anyway).
2. Use manual focus with PDAF focus assist - this will definitely work with Canon glass, I think (though I'm not 100% sure) that you can use this with legacy lenses as well.
3. Use live view mode for focusing (much like you do with m43). If you're shooting studio, this is a very viable option.
If you really want focus aids, the Sony NEX and Ricoh GXR (with A12 module) both have edge enhancement modes in live view to highlight high contrast areas, which can come in really handy with manual focusing. They will also allow you to use lenses you won't be able to use on the Canon, namely, M mount glass.
Wind, Sand and Stars.