A muffler is going to work better with the engine system as it is. You'd have to modify it quite a bit and have a ton of air and fuel going in there to have a straight exhaust be any kind of benefit.
There's instructions in this thread about how to throw on a Flowmaster, or any muffler:
http://www.explorerforum.com/forums/showthread.php?t=182514
The stock system has a resonator behind the muffler, though, so that quiets the exhaust down some too. You can either get a muffler shop to bend you new pipe without the resonator, or go to a parts store and either buy a stock replacement pipe or a performance 2.25" mandrel bent pipe. It'll flow better and be louder. I suggest the Dynomax pipe, you can get it through Advance or NAPA or any place that sells Walker or Dynomax exhaust products.
If you don't want to spend the $100-200 on a Dynomax or Flowmaster catback system, or go to an exhaust shop and have them do the work, you can just get a muffler you want, rear pipe from the exhaust shop, some extra straight pipe to fit between the muffler and rear pipe, and some clamps. Put it all together, then take it to a shop to have them weld on a hanger behind the muffler.
I hear the Flowmaster 40 is the way to go on those, not too many people are happy with the Delta 44s. The 40 should flow better, too.
Magnaflows are excellent straight-through mufflers. They get a lot of their noise reduction from weight and heavy materials, though, so sometimes they are quieter than Flowmasters, even though a Magnaflow flows better.