That makes sense I would just eliminate the rear channel and let the focals perform like they should. I kind of got talked into using the rears with the install even though they are still stock. You guys have amazing sound quality with just the front stage only? I know with the way they are set up they (the rear) are pretty muffled anyways.You don't have enough channels to run the Focal's active, so you would need to run the crossover for at least 2 on each channel.
If I had to run that setup I'd personally run the woofers active on their own channel as they need the most power, then the mid/tweeter passive off the Focal crossover on the other channel (just make sure there is new wiring run from the tweeter to the crossover modules) then when you are setting up the DSP you can experiment between using the mid and tweeter for the time alignment.