No, they don't control which get's rendered, and are used for editing only. Both will get rendered. Just do not forget to give each channel a unique name, and then back in the Material Tab, make sure you point that material to that UV channel:

You use the same name where my arrow is pointing that you gave the UV channel. That makes sure that material uses that UV Channel.
So do you see now? You can give one object like 14 different materials, each with it's own texture, and UV Map each face on the object if you want. Cyan did that with a lot of their complex objects. This way, you can use high detailed textures individually, instead of trying to "skin" the object with one big texture that has different things on it.