Are you talking about making payments to a room only reservation so it's paid in full prior to arrival? Or are you wanting to pay over and above the room total to have a credit when you get there? If it's the first one, you have to make payments through your TA as they own your reservation until you check in. If it's the latter, I'm not 100% sure, but I don't think you can have a credit at the resort upon arrival. You can leave a cc at check in to have room charging privileges during your stay, but I don't think you are able to make payments to have a credit balance that you set up ahead of time.
Cruises are different in that the ships are on a cashless system, therefore, you can add money to your account prior to sailing to offset purchases throughout your cruise without having a huge bill to pay at the end. WDW doesn't work the same way and doesn't have anything set up to do that (at least not that I know of).