1. On the menu to your right there is an inventory section. In that section there is a 'Ships' link. Click that and your on the ship inventory.
If you own the ship, it should be in front of you now. Otherwise click on the Manage Assigned Ships tab.
2. To assign click the tick box to the left of the ship, then click the not very well named selection box at the bottom "Make over selected ships to:" and you'll see options such as Commander, Pilot, Commander/Pilot.
Pick what you want, enter the name of the person your assigning it to in the space that appears below and click Execute.
I'm not sure how clear i've made that but its pretty simple if your looking at it and clicking things anyway.