My Question is How should I be seperating the wires?? I have alot of the smaller gauge 16-18 gauge wires, and some larger diameter wires..should these be separated??
Check out these pictures and descriptions, might help clear up some confusion.
Copper | cedarcityrecycling.com

Also, is there an easy way to determine aluminum wire vs coated copper, especially the smaller stuff....very hard to tell.
Yes, snip it with a clipper and look at the bare ends, if it's copper then you'll see it.