Personally I connect my pump to the wpump header and set it to a fixed RPM. You don't usually need variable pump speed, just enough to keep everything flowing based on your loop's restriction and beyond that higher speeds don't buy you cooler temps. Fan speed matters far more.
Ideally you would use a temperature probe in your loop and use the water temperature to control fans speeds. That way when you get small spikes in activity you don't get fans ramping up and down. Water cooling easily absorbs those small spikes so you really only need the fans to ramp up when under sustained load(and thermal output).
If you're interested Jayztwocents has a recent video on some open source software that can control fans based on more than one input temperature. So if your rad fans are cooling both your CPU and GPU you might want them to ramp up if either of those components gets hot. I haven't tried the software myself but the potential to use multiple sensors is intriguing.
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