To make sure they stay separated, keep the water level a bit lower.
Circulation and heat... make sure that there are holes in the divider. I would like to figure out a way to use something like a nylon mesh so that won't be a problem...
Filtration: as long as there is adequate circulation, the filter won't work exceptionally well as mechanical filtration, but it should work well as a biological filtration. To make up for the loss of mechanical filtration on one side, I'd consider using a sand substrate, less than an inch, that way no anaerobic pockets and the crap won't sink into the substrate.