If the price of the flights goes down, you can call and ask for a price adjustment. You can call as many times as the price goes down, but only before final payment. Likewise, any changes you make have to be done before final payment. After final payment you will pay a change/cancellation fee.
If you cancel the cruise, your air can also be cancelled without penalty as long as it is before final payment.
Once you get the confirmation number, you can go to the airline's website and choose your seats. Also you can give your frequent flyer number and known traveler number to the Air2Sea agent to include in your reservation or enter it yourself on the airline's site.