You are correct. You can register your AKC female with CKC (Continental, I am assuming?) and have the litter registered with the CKC, but not AKC. This is what I did--I selected a CKC female and an AKC male...reg the AKC male with CKC (with his breeder's consent) and registered the litter CKC.
As far as the 'value' of the litter, from a monetary standpoint, you will find that AKC reg dogs do tend to sell for a bit more as it is a more established and recognized registry. However, as far as the 'value' of the quality dogs they produce...that is something not determined by a registy, rather the quality of the parent stock and how well their traits complement each other in the offspring produced.