Cool - Here's what you're working with:
Option 1: Let's assume you stick with a "2-into-1" system, which is what you currently have. Ideally, you'll want the downpipes (blue) to be somewhat larger. Next, you'll want them to fabricate a Y-pipe (green) that merges the two pipes into a 3" collector, which will look like this:
From there, I'd recommend a 3" diameter, 14" length Magnaflow resonator (where the current muffler is). The 3" piping would then continue back (replacing the pink pipe) to a 3" in / 3" out Magnaflow canister muffler.
Option 2: ALTERNATIVELY, you could maintain a true dual system. More expensive, but should make a little more power (and look awesome). Basically, both downpipes (blue) would dump into individual 2.25" - 2.5" pipes (replacing the Y-pipe). Then, an X-pipe, which looks like this:
Off that, a pair of 2.5" diameter, 22" long Magnaflow resonators, then the 2.5" pipes would run over the axle and back to the rear, capped off with a pair of small Magnaflow canister mufflers, one on each side of the rear end... and of course, two pipes out the rear.
The shop should be able to price that out pretty accurately, then it's up to you to decide which route to take.