It's best if you can get a dual in that matches up to the factory pipes, otherwise the shop will make a Y-pipe before the muffler, which usually isn't as good for performance as having the muffler be where the flows meet.
2-into-1 is much easier to route out the back, though duals are possible with smaller diameter 2" tubing to follow the stock routing out the back and between the shock and sway bar. Usually the problem is the tubing for duals will be too large, or at least larger than you'd need for a dual exhaust on a V6. It is possible for the shop to use a reducer or expand some pipe and make dual 2.5" exits on the muffler change to 2" dual pipes.
I would say a 2-into-1 with a 2.5" outlet and single 2.5" pipe out the back would be your best bet for a system that sounds good and performs good, but doesn't draw any attention for anything other than it's sound.
The "lightning style" side exit is very doable (with either single or dual exit), but the shorter pipe length makes for a louder exhaust, and you'd have to check the local laws on the legality of a side exit. Not all cities/countries allow for an exhaust in front of the axle. Keep in mind it will also be louder IN the vehicle with the side exit, the muffler placement on Explorers already makes it real easy to get exhaust drone inside the cabin. This can be annoying if you do a lot of on-road driving.
Dual outlets don't affect noise all that much, you'll get a pretty mellow tone if you have a dual-in/dual-out muffler that has an "X" cross-flow inside to equalize the exhaust pressure.
It's most important to have the right size pipe, since you can have a VERY loud exhaust with big pipes, but it will only be loud..the pipes will be too big to allow for proper flow.
My suggestion would be for either single 2.5" pipe or dual 2-2.25" pipes after the muffler, but if you go with a side exit in front of the rear wheel, you can probably just do dual 2.25-2.5" pipes.
Be sure you get some kind of performance air intake, too. Otherwise it won't take advantage of the new exhaust.