I set up companion rally points, ie "Att 1" and "Troop 1", like eferraro said.. Select "Fleet" so its automatic when they get there. Nice addition in v 1.1 beta is you can move your rally point, no need to disband, make a new point, disband, etc. etc. I launch my ships and then select the rally point instead of using a colony rally point but that is just a precaution by me as I change off production alot to manage my population and I end up with mixed fleets by accident.