If those cut wires were originally from the Tuner Plug, then yes you need to hook them up there to make things work. Check out the Tuner Plug wiring diagram here:

Diagram:


Key:


The blue wire on the right, if that is coming from your Empeg Sled then yes, thats not connected up right. That wire is supposed to be 'Amp Remote' which goes +12V when the Empeg powers up so your amplifier knows to turn on.

The yellow wire from the car harness is probably 'Memory' which is the permanent +12V that the Empeg should be powered by. If you have a VW or derivative Memory and Ignition Sense may be swapped over.

Note: There are probably two Blue wires from your Tuner. One is supposed to be on the Tuner Plug. The other is hanging free - this one is the Antenna Remote wire which goes +12V when the source is switched to 'Tuner' on the Empeg. Use this for signal boosters and those retractable electric aerials if you need to, else tape it up and tuck it away. Don't mix them up.