Even if you pick up the car at the Car Care Center, you can book it so that you can drop it off at the Dolphin hotel. My advice is that you price out the car several ways:
pu/return from car care center
pu/return from Dolphin
pu - car care center; return - Dolphin
pu - Dolphin; return car care center
I say this because the prices can vary and just so you are aware at the Dolphin hotel even if the rental desk is closed you can return the car by leaving it with the hotel's valet. They will give you a receipt that you returned it. You can then just hop on a bus to one of the parks or go out the back of the hotel and take the boat to hollywood studios or epcot.
The only thing is if you book at the Dolphin they don't pick you up at your hotel, that's only at the car care center.
Also, don't forget to do a search online for coupons that you might be able to apply to the rental. And, you might want to also do a search to see if you can join the National's Emerald Aisle for free or whatever Alamo's club thing is called, that will save you money too. And if it's free to join, why not.