We had many problems with our boat which only has 2 warranty dealers in Canada so we got in touch with the warranty dealer in the states and were given permission to use another service dealer, the person who gave the go ahead has since been fired and now the company will not honour the payment for the work.

If it's a large enough claim you would retain an Attorney in the City where the warranty dealer gave permission. For a small claim you would file in Small Claims Court in that same City. Jurisdiction is where the Defendant does business.

You would also name the employee if person did not have authority to give permission. I appreciate that that's hard to prove (or disprove) but I would name everybody to protect yourself.

Doesn't the manufacturer have anything to say about this?

Did you get anything in writing ?