I have ball valves on my mash tun and boil kettle. Do I need to also put them on the output of the pumps I use or is controlling the flow with the ball valves at the kettle and mashtun good enough?
No no no. Don't ever control the flow upstream. Always control the flow downstream. Beer pumps are not self-priming and they do not like being starved of wort when running.
Assuming that you're using your standard March / Chugger beer pump.
Yes you control the speed of liquid movement with the ball valve on the pump output. If you have the kettle valve that feeds the pump partially closed, you run the risk of starving the pump and losing prime.
Also, if you try to throttle the flow farther past the pump than the discharge you may blow the hose off. Like if you are pumping through a valve at the destination. Always use a valve at the pump discharge.