You can set the warning value by clicking the 3-bar menu, General and it is at the bottom. If you are flying smaller sites you could bring it down to 25%, but I have experienced that when these batteries (in particular) hit 25% they can go down very quickly.
I use DataPilot. Example would be a 125 acre project I did with 75/75 overlaps at 250ft AGL. It took about 1.5 batteries on an OEM. The trick to getting better efficiency is looking at the Photo Interval value at the bottom of the Survey pane and checking and adjusting the flight speed until that value hits 2.0 seconds. I can usually run about 20mph. The logic of the program can be pretty conservative. I have run 1.5 seconds with good success. Of course it depends on altitude, ambient light and camera settings. When I get down to 200ft is more like 16-17mph. It can seem a little tricky, but they are static values that you will figure out. I figure that by making sure that an object is captured 4 times on each pass I know I am getting about 75-80% overlap.