Within the Battle Tactics research tree, there is a box called Commander Preset II. This research gives you the ability to preset the points in the commander’s Skill Tree.
This means that you can redistribute the points as you see fit, depending on the gear and task at hand.
While the most natural method of filling in the points is from the top, you are better off filling it from the bottom of the tree.
The way this is done is by filling each box from the top just enough to open the next one. When you have gotten as deep as you can, you start to fill the boxes in the tree backwards.
The reason why you want to do this, is because the biggest bonuses and boosts exist at the bottom thus increasing the effect of each point you have earned.
Please note that you might need to test this a few times in order to figure out the optimal filling pattern based on your exact number of points.