You need the controller somewhere between the panel and batteries. You can arrange your desired amount of voltage drop on each side of the controller by choosing fatter or thinner wire for the lengths you have.
Also you can make up for voltage drop at the battery-controller end by jacking up the controller's high voltage set point for where it starts controlling.
this is a good guide for some of that work.
http://www.calculator.net/voltage-drop-calculator.html?material=copper&wiresize=2.061&voltage=12&phase=dc&noofconductor=1&distance=60&distanceunit=feet&eres=8&x=42&y=5