GW,
Just to be clear... Are you talking about vacuuming with a hose or some type of cleaner? Or are you talking about how to run the pump normally?
Our pools and equipment are almost the same, so I'll tell you what I do..
I have my main drain only open about 10%, maybe a little less... (You may have to covers, but they are really only one drain...)
My two skimmers are open so that they each have about the same suction.. For me, this means that the valve for the skimmer that is farthest way is open more than then skimmer that is closest to the equipment pad.. My guess is 70% open for the far skimmer and 30% open for the near skimmer.
I run my pump 24/7 at 1250 RPM most of the time.. (Note that running 24/7 is not a requirement, it is just a personal choice for me.) I like that I am making a little chlorine all the time and that I am skimming all the time.. I do ramp my pump speed up to 1500 RPM, 3 times a day for an hour, just to help with the skimming, but in the big picture I don't beleive it makes a lot of difference one way or the other. Another reason that I run 24/7 is that it makes the programming for the EasyTouch simpler and I never have to Prime my pump..
It takes about 1100 RPM to close my SWCG's flow switch, so I run at 1250 just to make sure it stays shut. Running less than 1000 RPM is not advised...
Skimming will just removed what is floating on the surface.. I have a Robot to vacuum my pool. Basically it runs off of low voltage DC and sucks all the dead bugs and whatever off the bottom of the pool. It also goes up the walls and cleans the waterline tile..
Please let me know if you have any questions.
Thanks,
Jim R.