You can do duals if you get a T56 and a custom-made crossmember. You'll have some decent ground clearance that way.
But you'd still get better ground clearance by running a single.
Here's my single 3.5:
I'd suggest getting it run over the axle if you want to lower the car. But if you are fine with stock ride height, you've got plenty of room to tuck a muffler back there.
Unless you run over something larger than a 2 liter bottle, you're good to go:
But if you're gonna use the 4l60e, you're gonna need to go with shorties to get decent ground clearance near the front of the car, so you may as well just stay with a 3.5 single to begin with.
This was how my dual 3inch setup was:
There's only so much space between the crossmember and the ground... and you can tuck up that 3 inch pipe as high as you can, but it's stil gonna take up 3 inches of space.
Also cross sectional area comparison:
single 2.5 inch pipe = 4.9 sq inches
dual 2.5 inch pipe = 9.8 sq inches
single 3 inch pipe = 7 sq inches
dual 3 inch pipe = 14 sq inches
single 3.5 inch pipe = 9.6 sq inches
single 4 inch pipe = 12.5 sq inches
That may help you a bit. A single 3.5 is about the same as a dual 2.5