To get back to the original question, where you place the holes depends upon what you want to get out of the closed loop.
The design you have is fine, if you want a large flow from the back of the tank.
What I wanted out of a closed loop was circulation along the sandbed surface, so I draw water from near the top of the tank and return it through a long "spray bar" run down the middle of the tank, just above the sandbed.
BTW, if your goal is general circulation, you may want to use pumps like Vortex or Tunze that can create almost random flow patterns when used with a controller.
When you plumb your pump I highly recommend using true double union valves on both the intake and output from the pump. This allows you to close the valves and remove the pump for service or maintenance, or even replace it.