You can't really "pre-order" a car. Some dealers will take money from you to hold a place in line so that you will be the first (or one of the first) to receive one of their allocations.
Some dealers will let you "custom order" a car once the order window opens. They take one of their allocations, go into the system and let you pick all of the options (colors, packages, etc.). They place the order and when it shows up (varies from manufacturer to manufacturer, with 8-12 weeks being about average) they take your money and off ya go. You can usually negotiate a price at the time of a custom order as well.
In my experience paying to hold a place in line just takes away my negotiating power and forces me to pay more than I am comfortable with. If they all sell out because this car is super popular then I wait until they build more. I am not "getting fleeced" because I wanted to be first.
