Yea, you definitely want to split the hops up.
I have done this split pot method for many batches and had no problems at all. It was fun. The clean up of the kitchen afterwards was a breeze too. (Ok, that last bit is a total lie.)
On Tap: 1. Kelly R. IPA, 2. Roter Hund Hefeweizen, 3. Bud Killer Blonde, 4. Red Dog Pale, 5. Roter Hund Oktoberfest, 6. Pumpkin Ale, 7. McRed's Stout (with new nitro system and stout tap,) Cream Soda, 8. ESB # 3, & 9. Ordinary Bitter.