[ngrubich]

There was a huge discussion about this topic not too long ago on here (and people over on reefcentral like to argue about it as well), but either way, as long as you put the ball valve on the return side of the pump (output), you will be fine.
With that being said, you get better control of flow rates with a gate valve over a ball valve.

 

[All your base]

It's pretty straightforward. Restrict the pump's output, and you're reducing the work the pump does, which results in less power draw and less wear - though the decreases will probably be within the margin of acceptable variability for something like a small mag drive pump.

Restrict the intake side, and you run the risk of causing cavitation, which can result in a huge reduction in the pump's reliability. This isn't a given with a restricted intake (it depends on the specific mechanics of the pump and the head on the output side) but it's a very real possibility.