This is my understanding. Someone correct me if I'm wrong. I think you may be confusing backpressure with scavenging. A larger pipe may not scavenge as well if its too big. I believe it has to do with heat, and too large of a pipe will be cooler and not scavenge as well.

It has to do with velocity. (and pressure waves)
Heat any gas and it expands.

Hot gasses better fill the pipe and keep velocity up.
The moving gas has inertia, the same as in an intake.
And you don't want your runners too big or you lose efficiency.

The inverse is also true...
Allowing a gas to expand lowers it's temperature.
Anyone who has used an air tool for a long period of time knows how cold it gets. (the gas expands and returns to atmospheric pressure at the tool)

This is how any mechanical refrigeration works as well.

So would it be better to have two smaller pipes rather then just have one 3 inch pipe.

A 3" pipe will flow more than two 2" ones will, if that's what you're asking.

Simple chart available here: How To Calculate Muffler Size and Exhaust Pipe Diameter | Exhaust Videos

Glad I found this thread. Don't want to hyjack but I am also in the market for doing my exhaust. And this has had some great info in it! I hope it's ok that I am posting here instead of starting my own thread again, if I am doing it wrong please let me know!

At the moment my stock ypipe is going back in and I need to figure out a good muffler to get. Was looking at a magnaflow so it would sound good and hold up and not be too loud in the cab. If anyone can link me to one they got that would be great! Thanks!

This is the one I have? I have one cat and 3 inch pipe back from it to the muffler currently. It sounds good, but is a bit mellow. If you have both factory cats, this muffler will not sound much different that stock probably. Are you going to have stock, aftermarket, or no cats?

After my engine swap, I'll be switching to true dual exaust with a pair of Dynomax Ultraflo mufflers.

http://www.summitracing.com/parts/MPE-12388/

Thanks TexasGuy! I'll have to see which one I will end up with but I"ve got some time to think about it. In the end I want to end up with a catless y pipe and then magnaflow muffler I think. Right now my stock ypipe with cats is quiet enough. Just got that put back on today. Thanks again!

I am putting on shorties, magnaflow stainless y pipe, kooks 2.5-3 inch stainless transition, quicktime cutout, 3" dynatech cat, all tig welded together and a gibson stainless split rear exit from there back going in next