Okay, first I will assume that you mean Disney World and not Disney Land (since you are talking Park Hopper and different resorts), so I will work with that.
I suggest doing it all on your own...travel agents will probably not get you any better deal than you could pick up through Disney themselves.
Second, go to Disneyworld.com and look at their deals right now. I believe that they are offering the meal plan for free if you stay on property and book now (which is a HUGE savings)...it might be worth looking in to. Also know that you are able to bring any sort of food/drink into the park at any point in time, so you should always have snacks and drinks available for your boys.
Stay at a Disney resort. Not only is it often times just as cheap as staying off property, it keeps the "magic" alive for your kids. Their resorts are some of the neatest places your boys will ever stay at, and are worth every penny. Plus you get free bus transportation to the parks, free transportation from the airport, and really great pools for the kids to play in.
Definitely get the Park Hopper pass. You will want to be able to do different parks different days, and some parks won't take you a whole day (i.e. Animal Kingdom). Having the Park Hopper means you can eat where you want, go where you want, etc. any time you want!
Make sure you book restaurants NOW! There will probably be quite a few that you won't be able to get in to (as those restaurants fill up right when people can call 180 days in advance), but there are plenty of really great restaurants, so you are bound to find some you like!
My family and I have done Universal a lot, and while we like it, it isn't Disney. They have the new Harry Potter park, so that may make it better, but my guess is that it will be packed since that area of the park only opens this month.
I told another poster the other day, I have done Disney over twenty times now, so any other questions you have, please feel free to message me with questions. We have stayed at most of the resorts, and have eaten at at least 3/4 of the restaurants. Hope this helps and have fun!!! :)