Being that you have the pool/spa combo is a very good thing. The POOL circuit should be viewed as your general filtration and SWG chlorine production circuit. Set this circuit for a run time that is convenient for you and somewhat outside of your typical spa usage (not critical). The speed should be as low as possible to allow the SWG to operate while keeping the flow switch happy which will probably be around 1700 rpm (+or - on your plumbing set up).
To set up a SPA circuit: got to Menu>Settings> Circuit Names> Assign an unnamed circuit as SPA, return to Menu.
Go to Menu>Settings, Circuit Functions>Scroll to SPA, assign function to SPA and default heater to ON position.
Go to Settings>Intelliflo>Speeds>Spa. set at desired RPM (ie:3000)
Go to Settings>Intelliflo>Speeds>Pool> set at desired speed (ie:1700)
Go to Settings>Schedules>Pool> select runtime you desire (2 hours is probably plenty).
Set the desired temperature for the spa circuit so when in SPA mode, the heater is both activated and tops out at the set temp.
When you want to use the Spa, push the V (Valves) button to activate the spa. When done, push the V (valves) button to return to POOL (or AUTO mode if not on POOL schedule) to return to normal. No egg timer is required (i'm not a fan of anyway).
Now go to Sunplay.com or Polytechpools.com and purchase ScreenLogic 2 (P/N 522104) and make your life and programming much easier.