That's too bad on your situation. They definately should take care of everything that's needed.
About the waxing your car. That's ok to wax anything new. I'm sure they asked if they do that do you want a pro-profesional pack. Which includes
aint sealant,undercoating,fabric/leather protection & rust proof.
You can break it up or do the complete package. They would include in your car note or you can pay seperately.
I did that at one of my old dealerships.
Post how it turned out for you.
Welcome on board & congrats on 09 Accord.
A buddy of mines wife have a 09 EX-L 4 cyl. It rides good & very roomy in the back