Are you just hooking the just the heater core back up? Mine was the same way when I bought the truck bypassed. I was told it doesnt matter which way you hook it up. It works the same both ways. So I just hooked er up, works fine.
Side note, if you bought the truck with the heater core bypassed u can bet the acculator is broke, somebody disconnected it durring the summer where it wouldnt blow heat with the a/c on. easy fix, just takes a little time. http://www.blenddoorfix.netfirms.com/