First, let me make sure we're using the same terminology before I answer:
Contract - The contract number that is tied to your CCO user ID and your equipment
Maint Agreement - Your hardware or software coverage.
My understanding is that you cannot put your hardware and software on the same agreement for a number of reasons. But there is no reason that all of your agreements can't be put under the same contract number. Often, hardware and software will be on seperate POs, etc. and will end up under separate contract numbers, making things a pain. I would work with your Cisco rep to see if you can combine all of your agreements under a single contract number. I don't see why it would be an issue. If they can't do this with existing contracts, then in the future I would talk with my rep about ensuring that all future purchases get tied to the same contract number.