I use a fountain pump. I have several. For smaller tanks (up to about 20 gallons) the pumps that will run about 100 gph @ 4-6' of head are good. Slow enough not to disturb the substrate.
For larger tanks I use pumps that will move about double that.
I use tubing from hardware stores on the pumps and aim it along the surface of the water so it does not dig into the substrate.
If you should overshoot and find you have a pump that stirs the sand, you can cheat!
Sometimes a simple clamp like a cloths pin can be put on the tubing to restrict the flow a bit. Crimping with your hand works for short term filling.