d,
I assume that you only have two pumps...
The Pump/Filter relay would control the main pump, and your Aux3 relay would control the Jets pump..
If your goal is to save money on the electrical bill, it makes sense to replace the main pool pump. It does not make a lot of sense, to me, to replace the Jets pump, as it would only be used when you use the spa, and any VS pump would have to run at almost full speed anyway to make the jets work.
Assuming this above is true, then you would only need to move the wires on the Pump/Filter relay and the Aux 3 relay.
What is the "PG2000"??
Thanks,
Jim R.