Running both filters shouldn't hurt anything. I've been told many times that you can't really OVERfilter an aquarium, you just speed up the rate that you remove the ammonia and nitrites. I agree with Madame_X, run them both for a while until you can start to see some bacterial growth on the biowheels, then you should be able to remove the old one.
38 Gallon (Freshwater): 1 Green Swordtail, 3 Yo-Yo Loaches, 1 Clown Pleco, 1 Blue Gourami, 4 Otocinclus, 7 Cherry Barbs.
46 Gallon (Saltwater): 60 pounds Lalo Live Rock, 60 pounds aragonite sand, 1 Coral Beauty Angelfish, 1 Peppermint Shrimp, 1 Mushroom Coral, 1 Emerald Crab, various snails and hermit crabs.
10 Gallon (Saltwater quarantine):