If ultimately you don't like the valve/plumbing arrangement of your Polaris booster pump, you could do what I did with my Polaris 280..... I put the booster pump on its own dedicated plumbing circuit so it runs whenever it wants and no valves involved. Been really nice.
If you decide to ever do this, there are a couple issues:
1) The Polaris Booster WILL run fine on its own however it is a NON-self priming pump so you have to either fabricate a priming pot to place on the intake side of it, or make sure the intake is flooded if your pumps are below pool water level, or buy a priming pot. I built my own out of 3" diameter PVC pipe about 18" tall with a screw cap on top for manual water filling. Once it is all installed and primed the first time, you don't have to manually prime anymore.
2) While you are redoing the plumbing, I would recommend plumbing in a T fitting with a pressure gauge so you can keep an eye on the booster circuit. Got mine from Home Depot.
3) You will also have to install a strainer basket in front of the pump to protect it and the Polaris from debris as it no longer has the benefit of sharing your pool filter. Got mine from Graingers.
4) You will need a spring check valve before the Prime Pot to help priming if you use a prime pot.
I connected my Polaris intake to my Pool main drain. Works great.