[Alneyan]

You do need to set the ship strategy (for the troop transports) to Capture Planet. To do so, go into the Designs screen, and hit the toggle Stats/Strategy. Then select your Transport design, and you will see its stats and the default strategy. Change that strategy to Capture Planet, and you are set.

Theoretically, it is supposed to work if your fleets stay in formation, and if the fleet strategy is "Capture Planet", but I do not think it works. That, and fleets should be set to "Break Formation" whenever possible.