I did a lot of research on this prior to doing mine. You can get 2 mufflers under there without too mcuh problem. If you look at the size of the stock muffler, it's HUGE. Just cut the pipe back at the cats and you're fine. 2 PVs are about the same size as one stock muffler. Then snake your pipes back to the sides of the gas tank and you're set. OR, alternatively, you can get a Flowmaster 50 series or equivalent - one in, 2 out. That's what I did. I've got ~2.5" in, dual ~2" out. It's cheaper and easier to install, although the power gains and exhaust note likely won't be as great as a true dual system.

As for the original question: $350 for a dual system isn't a GREAT price, but it's decent. It really depends on the muffler that they're gonna put in. For a FlowMaster dual setup, it's about average. You could probably go down to a local garage and have them do the same job for $250 - 300 though.