Ericscher,I don't have a camper top, but there are a few folks here who do.
Mostly they seem to leave them on full time and just zip out some panels. It would seem to be a fairly involved process to get the camper all set up, which is probably why they just leave them in place.
For the most part they seem to be a way to extend the season, especially for those boaters that like to fish.
This next part is just an opinion and it's worth exactly what you're paying for it...
Pontoon boats are a lot of fun, and they have it all over traditional boats when it comes to floor space. But... I'm not sure I'd want to spend the night on one if I didn't have to. Even allowing for air mattresses and a fair amount of effort to make things comfortable, it's still a pontoon boat.
Pontoons are best as a "platform", a means to an end.
They can take you and your friends to bars/restaurants all over the lake, they can pull tubes and even skis these days, they serve as mobile swim platforms and sundecks, and it's just plain fun to sail aimlessly around the lake. And they're affordable, as compared to traditional boats; but they really aren't house boats.
Having said that, maybe it's just you and your S.O. and you'd consider the whole thing to be romantic and fun. Or maybe you have kids, go camping a lot and are used to cramped living environments with minimal toilet and bathing facilities.
I guess my advice is; think beyond just the camper top. Once you have it in place, what will the practical aspects of your boating be, and are those things agreeable to you?
And good luck.
That's easy... F550 Crew Cab, pulling 35' Toy hauler with 6000lb towing option. Place seadoo inside toy hauler. Tow Benny behind toy hauler. Just don't drive down any dead end streets