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It's not a problem. You just make one pattern for each of the centrifuge results. So if you have two results that you need for your recipe, It'll centrifuge twice, then get some extra which it will use immediately the next time you ask for that item.
Keep in mind the production rates with centrifuging things. Not everything is guaranteed, so you may want to utilize level emitters to automatically centrifuge things for you when chance-based items are below your preferred threshold. You can see the percentage chance of an item being produced if you look at it in NEI. Some combs produce X item at 25% or lower per attempt and AE probably won't understand that.
