This will probably sound like a stupid question, but I don't know what the auxillary batteries are for. What do they do? What does auxillary do overall? I keep getting the batteries and end up selling them because I don't know what they are for. Thanks!
Alot of science powers run off aux power. The higher the aux power the more effective those abilities. Aux also increases turn rate. Very handy if you are say, a battle cruiser that finds yourself a bit too close in to a fight.
There's really not that much use for them on a 5 minute shared cooldown. However, if you're going to be getting into fights where you know you won't need a shield battery, you can pop an aux battery right before using tachyon beam or sensor jam (2 of the more popular Sci skills). The battery will dramatically increase the amount of shields drained from the target or the length of the jam (as long as you use the ability within 3 secs of the battery).
Play around with them. They are the "most fun" battery to use since a lot of the fun sci skills get a big boost from them.