If the key has a Chip in it, it has to be programmed into the system. Unless Ford has done something funky with the onboard computer, you should be able to program up to 8 keys/fobs into the system.
This may not work on the GT, BUT, get in the car and close the door. Insert 1 chip key into the ign and cycle from the off to on pos, like 7 or 8 times in rapid sequence. At that point, the cars door locks should cycle from lock to unlock, then insert the next key, cycle once from off to on, insert next, etc.
Key program at the same time, you just hit the lock button once for each fob.
after all is done, turn the key to the off position and remove key. everything should be prog'd then.
This will also remove any keys from the system that may be "floating out there" from previous owners, or dealers, bank repo people, etc.
The owners manual should cover these details somewhere.
If you only have 1 chip key, then the dealer will have to program 1 additional key into your car using their STAR Prog tool. It should be less than an hour, and you should be able to get blanks off Ebay for cheap(welp cheaper than the dealer). Have a local locksmith cut the key, and ask the ford dealer to just prog the key into the system.
For my Cobra R, it cost me over $ 150 for my 2nd key.
Also, if you just want a key to open doors, trunks etc, you can get a blank from anywhere and have it cut. It won't start the car, but if you lock your keys in, you'll still have a way in. Also I've seen the plastic keys on a card that fit in your wallet, those should work as well, providing your locks operate in a smooth manner.