What Polaris model do you have? All the ones I know of are pressure side, so it shouldn't have any impact on the skimmer suction, unless there's an automated valve somewhere (which wouldn't be common). The booster pump creates a higher pressure (and lower volume) stream to the Polaris. There are models that don't need a dedicated boost pump (e.g. the 360), but my impression is that they don't work as well as the boost pump versions.
You most likely don't need to run the main pump at 3450 for the booster -- the main pump is basically run to ensure that the booster pump stays primed. I have old non-synced timers and have accidentally had the booster on without the main pump (DON'T DO THIS!!!!) and it hasn't run dry and the Polaris seemed to be running properly (again, DON'T DO THIS!!!). I run my VS pump at a low speed (1500RPM) even when the boost pump is on. I'd try it lower while watching for air in the lines, ensuring the cleaner is working, etc.
Is it possible that with the main pump at 3450 the pressure out of the returns is so high that it's not creating a nice even flow toward the skimmers? If you run at 3450 with the boost pump off, how does it work?