Just moving your ships on top of one another will fleet them up, if you have the logistics.  You also have the "Manage" button in the lower-left, if you have ships stacked together.  However, neither method always works if you have a Fleet Commander in your fleet.   It's buggy.  You just have to keep trying until you figure out what works.  You'll get it eventually.

Anyone else notice the bug in standard 2.5?

Now when you have a stack, the ship/fleet you are directing is NOT shown as the top of the stack.  You have to look at the fleet/ship box in the corner to see which one is "active".

Also, when cycling through idle ships, sometimes there is no circle highlight to show which ship is active.  Which can be very tricky when you are zoomed out or have a lot of ships in a given area.