They will take care of you regardless of whether you are doing an all cruise or a "land and sea" vacation. If you are working with a
travel agent, you will tell them what you need, and if not, you will deal directly with Disney reservations. Either way, ask for written confirmation.
Regardless of how you do it, your travel agent or Disney will tell you the room numbers of the staterooms that match your needs so you can see where they are using your handy deck guide (see
www.disneycruise.com).
Accessibility for shore excursions is another story. You are better off posting here saying what you would like to do and what your needs are to see if anyone has experience. The excursions are not run by Disney and they tend to have lousy info on accessibility, and non-US ports are not subject to the ADA. There are good options, but you will tend to do better asking around rather than relying on
DCL, in my experience and based on what I have read.
I love the
Disney Cruise, you will have a great time! Feel free to ask any additional questions.

Cupcake