Apologies - I missed this yesterday. Welcome to the DIS, jennarobert.
I haven't heard of any "system" per se. In my experience, it's always cheaper to book the separate elements of your trip independently, including booking WDW hotels directly with Disney (or through a TA such as
Dreams Unlimited who will, in turn, book your room directly with Disney). That way, you can always request an upgrade at check-in. The cost of an upgrade will depend upon availability and the prevailing rate compared with the price you've already paid. For example, we paid for a Savannah View at AKL back in 2001. We received a discounted Annual Passholder rate (which, incidentally was a fraction of what we'd have paid by booking a package through a UK Tour Operator). At check-in we enquired about upgrading to Concierge and, because the rate had reduced since our initial booking, we were able to do so for $20 a night. Job done!
Whilst upgrading from a Value to a Moderate (or, similarly from a Moderate to a Deluxe) is theoretically possible at check-in, it seems to me to be an odd thing to do. Provided you've booked direct, it would make more sense to attempt an upgrade before you fly.
From what I've gleaned over the years, those who have booked packages have invariably found it impossible to make any alterations directly with Disney. I'd be interested to hear of anyone who's achieved it.
