Are you staying at a Univeral hotel for FOTL? That is the best thing ever created, I might add.
I don't think it really matters, it depends on your family and what they are looking forward to the most. We started with Universal on the first day, then did IOA on the second, but for no rhyme or reason, really. Check out the attractions for both and see what you're more anxious to see/ride! They have some kickin' rides there. =0
I should say that if one day was, say, Saturday, and another was a weekday, then I would avoid IOA during the weekend...