Prep fees are not doc fees. If you see a prep fee on your invoice you have been ripped off. Dealers are paid by manufacturers to prep the vehicle for new car delivery. Documentation fee is also another goofy fee dealers put on but I normally don't care about if it is not more then $199. Stay away from window etching as well. Some dealers will tell you you MUST do it, you then tell them to screw off. It is a waste of $xxx since when was the last time you heard a window was stolen from a vehicle and recovered because of a window etching. If you are super concerned about theft, get Lojak!
If all is done well by your dealer you should see doc fee, MV fee, Tax, rebate(s) and negotiated price of vehicle on the Bill of Sale (also your trade in allowance if any)