It would be very simple for me. I would literally have everyone involved in something. From CM Punk, all the way down to JTG. You have plenty of TV time, I say you keep one angle (maybe two) that will be played out on both RAW & Smackdown, while using the rest of the tv time to give the other wrestlers in angles / storylines.
I know this is a pipe dream but, this is one of the few things I miss about the Crappitude Era. Everybody was at least doing something (even dancing around in a speedo and a fanny pack, is better than nothing.)