So today's my online check in and I don't have our passport numbers (they will be here any day, so no worries) can I just put in my driver's license number and change later?
This. The website can't recognize that whatever you enter is a "correct" number, it only recognizes that you've entered something. You can go back to the check in pages later (prior to 3 days before the cruise) and fix any "errors".
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