Flappers, or rain caps or whatever you prefer to call them, just clamp on the top of straight cut stacks, pretty easy.
I used to think the flappers were the coolest thing when I saw them on big trucks, but I've seen a few pickups with them and they just don't look right, on dual stacks at least. I think a single stack would actually look better with a flapper than any other kind of stack.
By the way, a couple companies make "quiet" flappers and you might want to look into those, otherwise they clang-clang-clang at idle. Lots of places sell the flappers though. There are some on ebay, or at airflo.com (that's where I bought my stacks)
BTW, I used to be real iffy on stacks too, but I bought them on an impulse over the summer. Now that they're installed, hell, I love em and I think they look pretty cool, and three guys at work told me they looked pretty cool within 2 days of me installing them too
Now if I could just get the volume to a reasonable level, I'd be a happy camper.
For some reason I do feel like they look a little better with the toolbox installed...and I'll never have a camper or cap on this truck (it came with a cap when I bought it, I sold the thing)