Z,
Not how I would do it, but I don't see a major issue.
You should run your main drain at about 10% open and your skimmer at full open. You can do that with what you have and the IntelliValve set to VAC full off.
Then when you want to use the VAC, the IntelliValve moves to VAC full open and the main Drain just stays at 10%.
You really don't even need the main drain on at all if you don't want to.
Maybe I just don't understand the problem you are seeing??
Thanks,
Jim R.