You'll have to go to an interstellar factor that you'll find at the station under contacts in any low security system. He'll clear your bounty.
The normal procedure is to drive away from the base until you can see "recall ship" on your role panel. Your ship won't land if you're too close to the base. When your ship lands get in, take of, and then you can land at the base, but only if it's a landable one where you can get docking permission. Don't atempt to land on it without permission.
If you get a bounty at a base, be very careful about any patrolling ships. they'll probably start attacking as soon as it lands, when you're not in a position to fight back. if there are patrolling ships, either drive a long way away or logout and back in again to make them disappear. Remember, it's no problem to get blown up in the SRV. You'll be put back in your ship ready to leave without losing anything other than any cargo that's in the SRV.
In case you don't know, also, if you park your ship on a planet, then drive too far from it, it'll take off by itself and go into orbit waiting for you to recall it from the role panel. If you come under fire in the SRV, it's better to dismiss your ship rather than try to get in it.