Ok I remember a programme when I was a kid that was puppets I think. It isn't terrahawkes, or starfleet. It had a princess in one ship with her big dog like creature and the baddy was a woman in another ship with one side of her face covered in this black eye patch type thing. It's buggin me so much because that is all I can remember and wonder if it really existed lol

Sounds like you mixed two
Series together

"It had a princess in one ship with her big dog like creature"
Starfleet X Bomber
And
"the baddy was a woman in another ship with one side of her face
covered in this black eye patch type thing"
Terrahawks