A simple automation like suntouch would eliminate any issues concerning certain elements of your system turning on with no flow. We have a customer who, against our advice, ended up with a VS pump and a booster pump that weren't linked with automation and he went through about 3 booster pumps in a matter of months before he took our advice and went with a simple automation.
edit: now that I think about it, Intermatic has a system that may fit in your existing enclosure. You might want to look at what they have to offer as well.
I agree that automation is the best way to do it, but I think I found a way to do with without automation. Feel free to shoot holes in my setup, but be nice about it! Fyi, I live in Jacksonville, FL.
In my garage panel I have two 20 amp breakers that run to a dual intermatic dual timer. Volts are 240. Both timers ran my pump, salt generator and my boost pump for my polaris. I use a harward DE3620(?) DE filter and i have 2 pool spitters at each end of the pool, that are manual - uses pool pump for pressure.
Old setup:
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Manual timer one controlled my single speed 1.5 hp floeTech pump and my aqua rite salt water generator. The 1st timer then fed the 2nd timer only when timer one is ON!. The 2nd timer is used for my polaris 280 boost pump. This is so the pool pump would be guaranteed to be on when the boost pump ran. I ran my pool for 8 hours on timer one(pump and salt cholinator) and timer two(boost pump) for 1.5 hours. This was my summer setting and my pool looked and ran great for 10 years. Now my pump started to loose pressure since my pool spitters would not get very high. I decided on going with the Pentair variable speed pump - 3 hp as a replacement.
New Setup:
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I left all my old wiring to timer one the same - no change. I took the L1 and L2 that was on timer one and moved them over from 2 and 4 to spots 1 and 3. What this did was bypass the timer function and gave power all the time to my new Pentair VS pump. Why? Because the Pentair has it's own built timer, you all know this. I now run the pool pump at speed 1 at 750 rpm for 12 hours a day 8am to 8pm. Timer one only controls my salt water generator and Timer two controls my Polaris boost pump. My timer one(salt chlorinator runs for 8 hours 10am to 6pm - same as old setup) and the boost pump still runs for 1.5 hours from noon to 1:30pm. You may be asking yourself if the saltwater generator flow switch works at that low RPM? Yes it does. Do my pool spitters work? No, pressure to low, so I turned that valve off and when I want to use them, I will turn the pump to 2300 rpm's and turn valve(to spitters) on manually. Is there a possibility that the three timers get out of sync? Of course, but that would probably be pretty rare. Remember if timer one is off, so is timer two and timer two has the boost pump, my main concern. The intermatic timers have never gotten out of sync in 10 years that i own them. Now as far as the Pentair timer, only time will tell, but i have enough buffer in the manual timers to offset any lose in power. Power would need to be off by 4 hours to effect my boost pump. My only real major concern was running the boost pump when the pool pump was off. I could run my pool pump for 24 hours straight just to be safe, at 750 rpms. The only very minor concern was the salt water generator flow switch failing and the saltwater generator running when the pool pump was off(very very unlikely). Remember my Salt chlorinator runs for only 8 hours a day and if there is no flow, it won't generate chlorine. What about the skimmer? I have two skimmers(probably over kill) and my pool is 13000 gallons. I only installed this setup yesterday, so i may have to bump up the rpms or turn off one skimmer. Let me know what you guys think about this setup. Eventually i will go to a home automation system...but not sure which one, but one that supports my new pump. Update to post: I was getting tiny air bubbles in my pump cover that got bigger over night. I read a post that says 1000 rpms should do the trick. 750 rpm is to low.