You didn't mention what company you're renting from.
If you're using Alamo or National, they have desks at both the Car Care Center and at the Dolphin. If you're staying at one of the Epcot reports, return at the Dolphin and just walk. (Or just plan on heading to spend the day at Epcot or the Studios right from there)
At the Car Care Center they have a free shuttle that will bring you back to your hotel, or to one of the theme parks.
Most other major companies have counters at hotels along Hotel Plaza Blvd. Some have free shuttles, others you could walk to Downtown Disney and take a bus back to your resort from there.
-Rob