You can add them to a fleet. Then they all work together.
Select one ship, and then click the 'Fleet Transfer' button, it has 4 ships and a +, (Or 'F' key), then click 'Create Fleet', and add the ships.
__________________
Creator of the Star Trek Mod - AST Mod - 78 Ship Sets - Conquest Mod - Atrocities Star Wars Mod - Galaxy Reborn Mod - and Subterfuge Mod.
Why? It works nicely as it is now. You want ships to be together, fleet them. You don't want them to be together, don't fleet them. I believe that "ctrl + a" selects all the ships in a sector when you are on the main screen. Now, what would be cool would be adding a way to fleet fleets. So instead of them being fleets, they would be squadrons (or something). Then, you would make fleets by grouping together squadrons.
You know thats a great idea - id like to send in seperate fleets to attack a target at once without needing to have then in a single massive fleet - the squadren idea is good. As would be being able to "lend for x amount of terms to an ally" specifc squadrons to attack an enemy on their other frontier or perhaps able to rent fleets from an ally - some ideas to work with that could be used to expand the game in many ways.