Make sure you are in the same location as the cicilian ship. This is normally easies to accomplish by having your tug wait at the colony that the civ ship is headed for and waiting until they get there and start loading/unloading, using small time increments as neccessary.
Go to the individual ships screen, select the tug, go to the Miscellaneous tab, in the tractor link box you can select the civ ship.
If you are doing this to get rid of ancient slow designs, give the civ line some funding to cover the cost of the ship you have requistioned.