1. Your soldiers comprise the new population of the planet after you invade it. The game (rather unrealistically) represents planetary invasions as involving the complete annihilation of the previous inhabitants, at least as long as you don't use Information Warfare.

One transport remains after an invasion for every 1000 legions ("troops" as most call them) that survive; all others are lost. From what you've said, it sounds as if less then 1000 legions survived and all your transports were lost.

2. While I don't know what happens to colonists on a colony you destroy - as I offload everyone on a transport first - I would presume they're lost with the planet. The game makes no distinction between "soldiers" and the general population, so you don't need to be concerned about treating the inhabitants of the planet separately.

I should note that the best way for you to deal with low-PQ planets in your space is to simply flip them to your influence, rather then invade them. Or, if the planet is so bad, simply ignore it. Also, many low-PQ planets can be terraformed into good ones if you research the techs, so you might want to think twice about destroying that colony.

Amen on that one. As far as I'm concerned there is no such thing as a crappy planet, There are planets that you don't have the colonization tech or the terraforming tech at the moment to make them worthwhile but if that's the case then it's easy enough to ignore them until you do get the colonization and terraforming techs to make them worth your while. In Dark Avatar I've never seen a planet improve to less than PQ8 and most planets that start out as PQ1's usually end up as PQ13 or better. Even in the Dread Lords version where there are a couple of PQ3's and a handful of PQ4's and PQ5's, I've never felt the need to actually destroy a planet although there are some you're in no big rush to take over right away.

What I meant is that each "soldier" on the invasion screen is a 'legion' consisting of 1 million soldiers. Thus a planet with 6 billion pop will be defended by 6000 "legions".

Yes. Also, one transport is lost no matter what. Thus even if (for instance) you actually end a battle with more men then you started with (because of Information Warfare) you will still lose 1 transport. This can be an advantage to attacking with fleets of transports, as surviving transports can then be used to invade another planet.

On the other hand, "wave" invasions involving one transport at a time are also effective because the more damaging invasion methods only take effect if the invasion succeeds. So you could use one transport to hit a high-pop planet with mass drivers, which will fail but take out most of the defenders, then send in another transport to finish the job with a less destructive invasion method.

A legion is 1 million soldiers.