CO2 Affect Conditioning?

I like to condition my beers in the keg after a few weeks in a carboy. Should I wait to start caring the beer until it’s been condition? In other words, does carbonating the beer affect the way it conditions, or impair it in any way?

I assume that by “conditioning” you are refering to the yeast settling out. You might as well carbonate if you are using natural carbonation (also known as conditioning, hence the confusion). If force carbing you would also do this before the yeast settles since it will stir up the beer somewhat, especially if you hook the gas to the “out” post.