Unless someone has a massive cheat code for the MiniDSP, it only has 2 inputs. If you want to manage your subs and mains on one MiniDSP 2x4 you'll have to run full range out of your AVR, into the MiniDSP, and two channels to an outboard amp, and the other two to your subs.
I'd rather have the dedicated LFE channel.
Also, tweaking your mains should be done with incredible caution. I'd only cut levels and boost nothing. Your subs have all sorts of digital limiters and DSP on them to prevent damage which your towers do not have. As Tom at PSA said, "don't take it as some sort of challenge, but you should be able to tweak all you want without concern."