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1. Does the bus stop at the airport in cancun
Yes. It will stop at Orange Walk, Corozal, Tulum, Playa del Carmen, Cancun airport and then terminate at Cancun City.

2. Does the bus leave where the water taxi comes in at?
No. You have to go from the water taxi terminal to the bus terminal (still called the Novelo's terminal after a former bus company). The distance is about 1 km and an easy walk along sidewalks through the downtown area of Belize City, but you can go by taxi for about BZ$6.

3. Will I pay for the entire trip in Belize city or does it still split payment so you pay the majority in Mexico?
I think it is still split, but please report back and let us know.
In Belize City (and in the rest of Belize), you can pay with US$ (if that's any help), so you can get rid of your BZ$ as soon as possible and use US$.

As for exchanging currency, money changers usually wait around the Belize Immigration building -- I've found the exchange rates very fair, certainly better than an airport. I don't know if they will still be there at the time when the bus goes through (about 10:30 pm).

Don't forget the departure fee when you leave Belize -- BZ$37.50. It can be paid with BZ$ or US$ (US$18.75). There will also be a tourist fee when you leave Mexico -- that's 294 pesos and can be paid at Cancun airport.

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The fare is still split (well, as of two weeks ago), with BZ$19 paid in Belize and the balance paid at Bacalar in Mexico. I paid the balance in Belize dollars.