Nail down the total cost of the car that goes to the dealership - that includes the negotiated cost of the car, transportation to the dealer, "prep", any added equipment, and documentation fees, less trade value for your old car, if any.
"What number would I write on a check to get the car?" includes all that. Your $500 deposit counts against that total. How it breaks out is immaterial - it's the total that matters.
This doesn't include fees to the gubm'nt like title, taxes, and tag, which are separate (but in some states may be collected by the dealer at time of sale, but usually(?) are a separate transaction with the DMV, but you should have a reasonable idea what to expect before going in).
Requiring a deposit on merchandise you're special ordering is not an unreasonable request. It shows you're serious enough to make a financial commitment before they manufacture the merchandise (or take it off the open market) for you.