I'm wondering about the amp turn on output from the Empeg. Does that run directly to the amp

Yes, it should be connected directly to the amp's remote turn on wire. Just like any other stereo installation.

and if so, what is the amp turn on coming from the factory system for? I assume that it is an input to the amp, but it runs to the factory head unit???? There is no factory amp (which by the way, in Infinity systems is behind the glovebox, if you were wondering), so is that wire currently serving a purpose?

Assuming that your information is correct about that wire's identification: Odds are, that wire is not connected to anything at its other end. It would most likely only be used if the car had come with the premium sound system option. (A factory amp.)

In most cases, all of the various dealer and upgrade options on modern cars are plug-in affairs. So, to make manufacturing easy, every trim level of a given car will have the same wiring harnesses even if some of the wires on the harnesses aren't connected to anything.

For instance, you've mentioned that there are speaker locations on your car which have no factory-installed speakers in those locations. When you remove the necessary panels to install speakers there, you'll most likely discover perfectly good speaker wires waiting for you. If you get the right adapter plugs, you can plug your new speakers into those wires without having to cut them. Of course, the other end of those factory speaker wires probably don't go to your desired amp location, but that's for you to work out.