Player skills on mothership?
 

Well i just got the game, and i was wondering is there a way for my main char to use his skills while controlling the mothership? Or does he have to be in a fighter?

Yes mate they do.. If you drop you character into the chair and the ship surges ahead and turns on a dime then you have your skills in tune with your ship. If the ship coughs and farts then stalls your character skills could probably do with some work.;)

my problem is that i cant use skills like hacker 1 skill while hes in control of the mothership.

All passive perks work with mothership. All active perks don't. Of course there are some missile related perks which would work if the mothership could has any missile launchers.