The Disney site only transfers from one gift card number to another. You have to transfer the full card amount to the other card - you can't transfer partial amounts. That can get a bit tricky with the $1000 max limit on any one card.
On my WDW trips I usually carry 2 or 3 "blank" cards. I charge everything to the MB, then on the night before check-out, I check my balance on
MDE, go on the Target website (5% discount with a Red Card) and buy as many cards as I need to pay off the balance. I then go on the Disney GIft card site and transfer to the blank cards. I can then take those down to the concierge and settle up. I've only had trouble once when the Disney GC site would not recognize the blank card I was trying to transfer funds to. No problem - I took the gift card #s from my email from Target down to the concierge and she was able to settle up using just the numbers.
This method is far more secure than buying and carrying loaded cards as I have absolutely nothing I can lose or get stolen. I only have the gift cards for about an hour, and that is entirely electronic funds. It may seem like a lot of work, but I save about $100 a trip and that's totally worth it to me. I do the same thing when I pay my DVC dues so I get a 5% discount on those too.