You don't actually have any control over your units at all mid-battle, but rather use the time to see where the set up of your fleet is working, where your forces' weaknesses lie and changes are needed, and perhaps also to learn from the strategy of your opponent. "Setup of your forces" here refers to the fact that you can build some combination of different units into a fleet (option on main game menu), then you write little AI scripts for your groups of units (using Notepad or Gedit or another text editor of your choice) and then start up a battle between a few different fleets and see who wins.
If you can't be bothered with the fleet editor or writing AI scripts right now, and just want to see something happen, follow these instructions: