I don't know if the neoprene seal needs replaced just yet. Is it all torn up, or did it just separate at the seam?
I wouldn't use aquaseal unless you never want to take your repair off again (say the next time your seals decide to give up the ghost). I use this stuff on the outside of my seams - it's very durable.
There's an accelerator you can mix in with the aquaseal that will thin it out and make it even more flexible too.
For the neoprene seal glued on the edge (like a butt splice), I'd redo it using a band of material between the sleeve and the seal. This way, you'll have something easy to glue to next time.
You might get away with aquasealing it back on too. Just be aware that when the seal finally tears, you'll have to cut the seal off.