You have to do it in a Creative mode, simply:
load all the ships you want,
Pause the game (this is important )
Select half the ships
Press the menu button (bottom leftish)
Then press "Allegiance"
Then select an allegiance other than "1" (all ships are loaded as allegiance one as default)
Next select everything
Then from the same menu go to "AI"
Select something other than "None"
Finally sit back and watch the mayhem unfold.
You can add multiple teams to all fight at once, just hover over the "Allegiance" sections to read more about the options.