yah, colony ships are the only way to capture planets. (some capships have a colonize ability which makes them count as colony ships)
Before you can colonize a planet, you need to turn it neutral. There are two ways to turn an enemy planet neutral. You can bomb it to the stone age. (Which you seem to have figured out)
OR... you can reduce it's allegiance to zero. Every planet has an allegience rating. You can view information about the allegiance by selecting the planet and clicking on the info blobs to the left of the Unit Portrait area.
Allegiance is a percentage multiplier that affects all the production rates of that planet. So, if the allegience of a planet is 50%, the tax income you recieve from that planet is 50%.
Planets have a max allegiance that is determined by the number of jumps the planet is from your homeworld. This drops off fairly quickly. Which means a planet that is 4 or 5 jumps away may be capped at 35% allegiance. Which means you won't be getting much income from that planet.
Allegiance is affected by culture. You can create culture by building broadcast cetners in your gravity wells. Once you do this your culture begins spreading down the phase lanes. A planet begins to be affected by your culture as soon as it begins spreading down a phase lane that heads towards that planet.
Once one of your planets is affected by your culture it's allegiance cap rises an additional 10%, (allowing you to grab 10% more resources from the planet). And the allegience of that planet begins to rise.
Each race has a specific bonus for units fighting in friendly culture. TEC antimatter recharges more quickly, Vasari i forget, and Advent gets a boost to shielf mitigation.
Now, if you can get your culture to affect an enemy planet, it will begin reducing the allegiance of the planet. If the allegiance of his planet drops to zero the planet will turn neutral and you will be able to colonize it with a colony ship.
However, this is usually a very very very slow process, the rate is determined primarily by the number of culture upgrades you've got compared to the number of culture upgrades he's got. It may also be affected by the number and placement of your broadcast centers. The key poitn of offensive culture is 1) to get the unit bonus to your units fighting in an enemy grav well. 2) to slowly chip away at the income he's receiving from the planet. and finally 3) if he doesn't do anything about, to eventually turn the planet neutral.
Another interesting thing about culture and allegience. The allegience of a planet is not affected by its hitpoints. So if you blast his planet to hell, but he's had culture to it for a while, it may still be at 90% allegiance. You cannot colonize a planet who has substantial enemy allegiance. (i don't know what the exact number is, but i think it's like 35%)
You can reduce allegiance to an enemy on a plant, by 1) destroying the broadcast centers feeding culture tot he planet, then waiting for the phase lanes to turn back to grey. 2) Bring capships to the gravity well. Cap ships immediately reduce/boost the allegiance of the local planet by a certain amount (i don't know what it is, or exactly how this works). If the allegiance is very high though, you may need to bring several capships intot he gravity well before you can colonize it.
Much more information than you needed to know, but I figured It'de be better to be thorough. I'm not 100% positive on a couple of these points, but it should give you an idea of how it works.
I'm going to post this on a new thread and ask for feedback.
