Hi Stacy! Congratulations on deciding to do your first marathon! The 2013 Disney World Marathon is the 20th anniversary of that race, so it is going to be even more special than ever!
For corrals--I would make sure that you put in the same estimated finishing time for both of you. That doesn't mean that you will be assigned to the same corral, but it will give you a good chance. If you are assigned to different corrals, you can both start in the latest one. (example, if you are C, but he is D, you can go back to D and start with him.) You just can't move UP corrals.
All of the Value Resorts are really nice. The newest one,
Disney's Art of Animation Resort, looks really neat! I think it would be really fun to stay there! If you plan to stay there, though, you may want to book way in advance! Dates there are filling up quickly!
I hope this helps! Please let me know if you have any other questions while planning your runDisney vacation!