[MisterBenn]

As mentioned above, races migrate only towards planets with atmospheres they can breathe, which makes sense. From what I've seen though, the migration mechanic doesn't especially prioritise moving a second race away so that the first can remain to undome the planet, which means it can take an age for the undoming to come about once a breathing races arrives, unless you intervene. I think an official patch should update this, so that people flood away from such a domed colony to take full advantage.

If a planet has two races and you need to get rid of one to undome, your options are:

1) Wait for migration to take place as above.
2) Population transport. Still quite timely, if the planet is at full domed capacity you will have between 100M and 2B people to transport away (Balance Mod 1.12). Also it will cost you maintenance and these transports can be shot down or hijacked!
3) Eject the non-breathing population into space. (Ctrl-K) There's no gameplay mechanic to punish you for doing so, it's up to your conscience (or your empire's).
4) If you are playing the Balance Mod, you can enable the "Colony - Population" minister to automate step 3 whenever it's required. Once a second, potentially undomed race arrives on a planet, the minister scraps the other population immediately. This is what the AI uses, regardless of Empire personality type. Since as the game stands the "honourable" methods of undoming are not very competitive, I typically use this option.

Option 4 does have its advantages, it means that if for example you have access to 3 races of different atmosphere types, you don't need to worry about which population to load onto Colony Ships. Just load whichever is nearest / most abundant, and colonise as normal. The next turn, they are scrapped and the correct race has begun migrating there. The stream of MILLIONS of migrants a turn towards this new planet (assuming you have a race that wants that atmosphere type) vastly outweighs the benefit of making colony ships that travel far to collect the correct population, or have huge storage capacity, or even have higher tech cargo bays, and negates the potential bonus of using population transports to move people around afterwards.