The only difference between a valet key, and a master key is that usually one of the cuts(notches) on the key is different so you cannot open say the glove box or the trunk. This has nothing to do with starting the vehicle.
Now a transponder key is a key with a computer chip with a digital code in it, the code in the key must match the code stored in the computer in your car. Also on some transponder keys they also have a physical key, which you insert into a lock cylinder. So to start the vehicle the key must unlock the key cylinder, and it's code must match the engine computer to start the vehicle.
There are two ways to program the key to your vehicle, in one way at say a dealer, they use a scanner to input a pin number to unlock the computer, and have the computer memorize all keys you will be using to start the vehicle. Some computers will memorize up to 5 keys. As each key will have a different code in it, which the computer will then be flashed or burnt into the computer memory.
The second way to program the key is using a transponder duplicator, where the code of the first key is copied to the second key. The draw back with this method is that you must use special keys which themselves can be flashed, instead of the computer in your vehicle.
There are also manual ways to program the key without a scanner, these are called back doors, and they are used when a scanner cannot login to a vehicles computer because there is some reason the scanner or the computer are unable to communicate with each other due to various reasons, such as wiring problems, or software issues.
Be forewarned that some transponder keys that are cheaper online may not work with OEM keys, and sometimes when you program the new key, it will lose the code to the second key. So cheaper isn't always better in the long run.
I strongly suggest having the key programed by a professional, instead of the tedious methods of multiple button pushing, grounding out wires on the fuse block, and other methods the backdoor method may require. Usually it takes less than 20 mins to program a key, and then you will know it is done right.