First of all, I wanted to say that is a great idea that you are devoting 2 days to Universal, your boys are going to love it. I feel like I'm kinda of an expert on what kids love at Universal, I have boys that are 5 and 8, plus a daughter and we go several times a month.
In Universal, they are going to love Jimmy Neutron's Nicktoon Blast, Shrek 4D, ET, Animal Planet Live, Curious George Play area, The Woody Coaster, Men in Black and Jaws.They might like the Mummy, but don't push them if they feel like they aren't ready. I waited until my oldest told me he was ready to ride it, which took walking by it for a year.
Over in IOA, they will love Seuss Landing which has the Cat in the Hat, One fish, Two Fish, CaroSeussel, and If I Ran the Zoo play area. They will also like The Flying Unicorn coaster, Jurassic Park discovery center, Camp Jurrassic, River Adventure, Dudley Do-Right Ripsaw Falls, Popeye and Bluto's Bilge Rat Barges, Spiderman, and Storm Force. There are plenty of places to get wet that are just too tempting for kids at Universal and IOA, so it would be a good idea if they wore shorts that dry easily.
What kind of ticket are you getting? If you wait till you get here, you can usually get a good deal on the third day free if you have the time for it.