Breaker panel install
 

I've just installed a 100 Amp panel in between the 2 x 4 studs in my garage wall to run power up to the 2nd floor where I'm creating an apartment. I plan to run the wiring up from the top of the box. should I put in some 2 x cleats above the panel to staple the romex to so that the cable stays in the center of the cavity?

I wouldn't think that would be necessary. It can't be more than 4' to the ceiling, probably more like 2'. Just attach them to the upstairs studs.

Yes but, not necessarily for the reason you stated.

Keep your cables separated. If you bundle them you are not allowed to pull the full capacity of current through them.