[Drake]

During combat there's an orders button on the right hand side next to options - it's where you tell a ship to ram another ship, drop troops, etc...

If you aren't playing tactical combat, you must give your ship combat orders to capture planet. That might not kick into effect until all the weapons platforms on the planet are dead. I usually, if doing strategic, put the transport in a fleet that has capture planet orders. The combat ships kill the WP, at which point the transport comes in and drops troops.

I'm not sure if there's a more effective method. I haven't messed around with strategic combat much because the ships seem to do stupid things when left to their own devices. I probably just need to play with the strategies more. *shrug*

-Drake