The Steam version can be installed as usual.
Some players reported that the game at some point refuses to start. Steam apparently does start the application but the game immediately stops working (no error message). In such cases it may help to delete/fix the settings file
Game.prefs. You can find it in the following locations:
C:\Documents and Settings\(UserName)\Local Settings\Application Data\Gas Powered Games\Supreme Commander 2\
C:\Users\(UserName)\AppData\Local\Gas Powered Games\Supreme Commander 2\Game.prefs
Be aware that deleting it will cleanup the problem but also reset your progress within the campaign and all your settings to default. So it may be advisable to simply rename the file instead, start the game and see what the problem may be by comparing the newly created file with the old defective one. Usually it has to do with some of the graphics settings, that do not work any more.