Chris,
You just need to schedule your system to meet your goals.. My schedule would not work for you.
I run the Pool Circuit 8 am until 8 am 24/7.. at 1250 RPM
I run the Skim Low Circuit three times a day for an hour at 1500 RPM.. I tell myself it is to help skimming, but I am not sure it matters, as my pool seems to skim well at 1250.
You have a heater, so unless you have a bypass, you will never be able to run that low.
In my mind, the first thing you want to schedule is for your pump to run long enough to generate the amount of chlorine your pool will need.
Since you have a Spa, you may want to set up the Spillway mode, so that you can flush the spa a couple of times a day, instead of having a constantly running spillover.
Thanks,
Jim R.