Welcome aboard Kaleu
Basically, when returning to port, you must enter the general area of the port (ie: 1km, though this could be more or less..). Once you get close enough, you will see a flashing anchor icon in the top left of your screen. Click on that, and Refit if you want to just head right back out. Or click End Mission to come in and choose a different mission or loadouts ,etc.
As Magnum stated, talk to the guy with the moustache (he will have a speech bubble or exclamation mark over his head (depending on Mod) to get upgrades or change loadouts. Talk to the Admiral to choose a mission and go back out.
Also, head over to the Mods section to checkout some sweet Mods that will improve your gameplay experience alot.
Cheers, and good hunting
Krauter