I have a 2 speed pump, and a booster pump for my cleaner. I love my timer, Intermatic P1353. It handles my pumps perfectly. I set it for mode 4, which is a 2 speed pump, with a booster pump. The timer then ensures that the main pump has run for a little while before allowing the booster pump to turn on. It also ensures that the 2 speed pump in handled properly.
There are many different predefined modes, but that is the one I use.