When emulating, you need to do as follows.
Plug in the autoprom to the computer
Plug the emulation cable into the autoprom and into the ZIF in the ecm, making sure its in the right way. Red wire is pin 1.
Open tunerprtRT
Load correct XDF and ADX files
Load correct bin file.
Hit the button initilize emulation hardware
Hit the button upload current bin to emulator, wait for it to upload and say sucess
Hit the button verify emulator aganst current bin (Cant remember the exact name of that button)
Hit the button enable emulation.
You should now be able to start and run the engine and make changes on the go.