I use to take the kids on roller coaster vacations for two weeks at a time for years. All up and down the east side of the Mississippi to the coast. I became a pro at making the most of it (i.e. avoiding crowds).
1) First and foremost: Get there early, when they first open the gates!! The easiest way to avoid crowds is when they aren't there yet! Can't be any easier than that. Even with the onsite hotels getting in early, it's still pretty sparse compared to later in the day.
2) Go to the back of the park first. Most people enter a park and start to hop on rides right away, the back of the park will stay empty for a little while.
3) As the day progresses, work your way to the front of the park since the crowds will be working their way further back.
4) During the middle of the day when it's really busy, go hit the movie theater at City Walk and chill out.
5) Stay late, crowds will thin out.
6) There's some nice hotels easily within walking distance. I know you purchased a hotel on site, just tossing my comment out for others.
7) Tickets: I usually would get the park hopper (able to go between Islands of Adventure and Universal anytime). It's been a number of years since I went, but 3 days usually covers it. We usually did 2 full days, then maybe a 1/2 day for the final day. They run specials at times.
We never did the water park stuff, so can't comment on that. Never needed a fast pass or whatever it's called, we just learned to manage the crowds effectively.