One thing I do is under my Logistics command have a single 'Transport Fleet'. Within this I have several Cargo Groups, a Colonization Group, one or two Tug Groups, a Deployment group, a Tanker Group, etc. When I have need of their services I detach one of the groups, send it on its work, and then order it to rejoin the Transport fleet as a subgroup. This saves me the headache of having all of those as fleets visible on the tactical map atop earth, without having to fiddle with detaching individual ships and recombining them.