If there is enough material, you could add the plastic pieces required to fit the cover - I assume you still have your snaps on the doors and on the dash? If they're not there you'd have to add them too. Badgerman would be the definitive source here.
I use both a snap tonneau with a belt rail system on mine. I have a badger top and a tonneau with snaps. What I did was when I installed the belt rail I used snaps on the belt rail where the rivets attach the belt rail to the body. I had to adjust the spacing but it does work that way for me. I can't remember if the belt rail was predrilled or not but I just used the same holes that was in the body when it orignally had a snap top on it. When I bought mine It didn't have snaps so I added them when I bought the tonneau.
Now I have a tonneau with the belt system so I have a full tonneau with snaps that I am going to put up for sale much longer. Chris modified a tonneau to fit with my gutter kit that uses the belt rails.