Hi, L. :)
Is your son's diaper actually LEAKING, or is it just seeping onto his clothing/sheets, etc?
My hubby and I use the Prowrap covers with prefolds, as well. This is how we do it:
Lay two prefolds flat, one on top of the other.
Lay a fleece insert in the middle, toward one end.
Fold prefold over insert and then do angel fold as you normally would.
Be very careful to check the leg gussets to make sure that the prefold isn't sticking out or uncovered around the legs or around the waist.
For a nighttime diaper, you really need TWO prefolds plus an insert. But it may also just be that your little guy needs the next size up of prefolds.
There are three things it could be if he leaks otherwise:
#1) The diaper isn't being folded correctly. My hubby and I fold the prefold in the "angel fold" and have never ever had a LEAK. However, when my best friend changes our daughter's diaper, she doesn't do the angel fold and just smooshes it all in there. On two different occasions when she has done this, my daughter has peed almost directly onto her lap. So the fold matters.
#2) The diaper service may be using harsh detergents that are causing the diapers to repel moisture. The best thing to do in this case is to was the diapers in Dawn to strip the chemicals or detergents out of the diapers.
#3) You may need to change the diapers more frequently. Cloth diapers typically need to be changed every hour if you don't want them to pee out of their diapers :)
Hope this helps!