Did you build the marine battalion or the marine company?
You can assign your dropships to transports in the ship window. You just go to the dropdown menu in the top-right, with the ship selected that you want to be a parasite, and then select the ship you want to assign it to from the list that comes down. Then you click land/recover (whichever it was, I forgot). If they're fighter sized (500 tonnes or smaller) you can use the fighter squadrons window and assign all of them to a single parent ship from there.
In the future, if the dropship is fighter sized, add it to the primary troop transport's preferred squadron in the class design window, and then have the destination fleet for newly built fighters in the industry tab be set to the fleet with all of your troop transports. The new dropships will automatically place themselves inside of the hangars of the transports if there are any already existing in the fleet.