I've only been there once and it was with 3 kids all under the age of 4. But the adults were going to take turns riding some of the "big" rides but by the time we got around to them the lines were really long. Maybe someone else can be more specific but I would say a general guideline might be to ride the rides with the highest height requirements first. We also went on a Saturday which is probably way more crowded than the weekdays.
And they have a huge water play area so you might want to bring towels and swimsuits.
Honestly with two days there you should have very little trouble doing pretty much everything. If there are some of the specialized workshops your boys are interested in check the website and book online ahead of time, but otherwise, as far as rides...with two days, you should be able to do them all probably more than once.
If Indiana Jones is a priority, get there at opening and go there first...the line gets LONG midday. The roller coaster next door is the same way. But, by evening the park clears out pretty well, so going late/staying late could work too. There is a sports themed restaurant back there that has pretty good food (burgers/sandwiches/salads)and a kids only buffet that has make your own hamburgers/hot dogs, mac and cheese, fries, veggies and fruit too. We started in the back and stayed there until after lunch then worked our way forward and never had to wait much for anything.
As far as what to bring...your camera! And, if your kids are going to want to do the water area, bring swim suits/towels etc. But be warned...the changing facilities are very limited (like one bathroom over there) and they will get soaked(and so will you if you want to keep any sort of close eye on them). IF we do it (and I usually try to avoid) we do it last, change into swimsuits somewhere in the park away from it where there is more room and just go home wet when we are done!