I currently have the stock exhaust on but my friend gave me a flow master exhaust but it won't hook up to my catalytic converter because the flowmaster has two in holes and the cat only has one out, can I just get rid of my cat and hook it up to the two pipes going into the catalytic converter?

Ummm, no, removing the catalytic coverter is illegal here in the US and will cause you to fail emissions testing just for the very fact that it is not there when they look for it, not to mention that it no longer being there will (chemically) cause you to fail the test as well.

Give the muffler back or sell it and buy a muffler that is specifically for your truck.

well yeah but if I just didn't care about emissions than it would work just fine right?

Well, in that case, as long as all the pipes mate up with each other like they are supposed to then it will probably work.

You might want to put a back pressure gauge in the O2 sensor hole and check the back pressure before and after you do this, some engines get weird when they loose too much back pressure and try to stall.