We have done the rental car drop off on each of our four previous cruises. I believe that the drop off location has changed due to construction at the terminal since our last cruise in 2009, but that shouldn't matter. Once you enter the Disney Terminal area there are CMs at every step along the way to make sure you don't step out of line and mess the process up for everyone else

(actually they are there to be helpful and keep things moving). While you are still in the car, you will all have to show ID that will be checked against a list of those sailing to be allowed on to the property.
Here's how it has worked for us: At the drop off area, we unload the car. Since it is a rental, we unload everything in the car. DW keeps the bag that she will carry for the next few hours with our documents and other items we might need before we see our luggage again. We have a few small bills ready for a tip for the baggage handlers. DW and the kids enter the terminal as I leave to return the rental car. DW has all cruise documents and my passport to get me checked in. She also keeps the credit card that all on board charges will go on, since that is needed for check in.
She enters the terminal and checks us all in and gets a boarding number (that's the reason not to wait until DH returns).
I drive to the car rental location a couple miles away, stopping to fill the fuel tank on the car. Then I ride the shuttle back to the port. Occasionally there are enough people waiting for the shuttle that I have to wait for a second shuttle to come, particularly if there are large families who all went to the rental car location (instead of being smart like we are!).
When I arrive back at the port, the shuttle drops me off at a gate that allows me to walk to the terminal. At that gate I have to present my drivers license to allow me in. Once through security, DW can direct me to where I need to go to sign my paperwork and get my KTTW card.
About a half hour or so has passed while I return the car, so the wait to board is only another 20 - 30 minutes. Then it is through the Mickey ears, snap a couple photos, have your family name announced and head to Parrot Cay or Topsiders for lunch!