Yep, you're fine to just tri fold the prefold and pop it inside the wrap. My LO is 12 weeks old now and we've been doing this since birth very sucessfully. What kinds of wraps are you using? I've found Thirsties Duo are the best for dealing with poo explosions!
You can also use a nappy nippa to fold the prefold around your baby before putting on the wrap (or even use wool longies if you prefer). Some people also use prefolds to stuff pocket nappies. Prefolds are very versitile so it's just a case of finding out what suits you and your LO.