I have a 2000 F150 with the 4.6, currently my exhaust comes off the motor (Both sides) each side has the converters, then it comes to the muffler as 1. and out the muffler as 2 exiting out on the pass. side in front of the rear wheel.

This was all factory, but i must admit it looks funny to be.
I was thinking about bypassing the muffler and running the pipes out the rear. would this cause any problems?????

 

Two pipes in front of the rear wheel from the factory? Only Lightnings.

Anyway, you cna change it to dual out rear it you'd liek, with or without the muffler. I'd skip the true dual, though.

 

If you can do true dual (two pipes, two mufflers), that'd be awesome, but you need a cross-over pipe ("H" or "X" pipe) to provide proper back pressure and pressure balance. If you do just straight pipes with or without mufflers, and don't have a cross-over pipe, you'll probably actually lose performance. And if you're going to scrap the whole system anyway you should scrap the 4 stock cats and put in 2 high-flow Magnaflow cats (1 each side). And if you really want to make it humm, go ahead and do headers. But then you're getting expensive.

Also, if you're going to make the exhaust flow better, make sure you also get a kit for the intake side to optimize the gain.

edited to correctly show "X" pipe instead of "Y" pipe

 

Some folks love running an open exhaust system, and claim no ill effects after doing so.

I would be a little concerned about loosing torque though.

No matter what you decide, it shouldn't be that hard to convert back if you don't like the outcome.