Welcome to the forums DarkShikari!
Now as for your question...unfortunately there is no easy way to make room on all your planets, then add a single facility to them all at once. Yep, it sure would be nice, but as far as I know it isn't possible. What I end up doing is just starting at the colonies in a system on the far end of my empire then begin the process of scrap one facility, build Atmospheric Converter, move on to next colony and repeat. Yeah, it becomes quite tiresome after the first dozen or so planets, but reaps rewards later on when your min/org/rad production triples or so.
Hope you enjoy the game! (despite the occasional annoyance

) and I'm sorry I can't help you out.
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Courage doesn't always roar. Sometimes courage is that little voice at the end of the day that says "I'll try again tomorrow".
Maturity is knowing you were an idiot in the past. Wisdom is knowing that you'll be an idiot in the future.
Download the
Nosral Confederacy (a shipset based upon the Phong) and the
Tyrellian Imperium, an organic looking shipset I created! (The Nosral are the better of the two [img]/threads/images/Graemlins/Grin.gif[/img] )