Just to followup a little on what Zanthis said:
You can deselect weapons by clicking on them. If the weapon isn't highlighted, it won't fire. This way you can carefully destroy all the weapon platforms on the planet without destroying its facilities.
It is a good idea to send your ships with weapons to attack the planet. Once you have destroyed all the weapon platforms, satellites and bases, click on your transport ship. Now, go to orders and click on 'Clear all Group Assignments.' Next go to orders and select the option which is something similar to 'Set Group leader' then select the first combat group and whatever formation--arrowhead. What this does is make the computer select your transport ship and only your transport ship once you hit end turn. Now, move your ship to the planet. Press 'E' for end turn. Move your ship, etc until you get to the planet. Now, press Orders->Drop troops.
This will start up the ground combat phase. You'll see the numbers of his militia--hopefully you destroyed any of his troops when you bombarded, and you'll see your troops. The ground combat phase only Lasts either 10 or 15 turns? Sometimes, I've seen the battle go on for the max number of turns and not be resolved until the next turn.
Something very, very important to remember: If you win the battle, the game, of course, moves ALL your troops to the planet. So, if you want to go invade another planet, don't forget to transfer them back to your transport ship. It is extremely annoying to painstakingly destroy all the WEP's on a planet without destroyign any facilities then go to invade with troops and get the message: There are no troops on this ship. (You can just hear a Star Trek-like computer voice adding 'You moron!' to the end of it. About that time, you just want to NUKE the entire planet. Oh, sorry. Anyways, good luck.
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