This is SFC OP? And you mean a single player skirmish?
I will assume such in the answer below.
When selecting AI opponents, select BASIC. this will allow you to select specific vessels.
Selecting an AI team you belong to will give you allies. Selecting otherwise will provide enemies.
As there are several sliders, you can easily set up skirmishes that contain 9 vs. 9 for instance. However, you will only have complete fleet control over your own three vessels.