Is there a way to..?

[Suicide Junkie]

As far as I know, the order your ships are constructed determines the order they appear in your fleet (other than the designated leader).

This is one area that really need to be addressed in a patch.
Something like a "reorder fleet" button, just like in build queues, and preferably with a graphic showing the formation your ships are currently set to. (So you can tell that you want a PD ship in slot #5, one square up and two to the left of the leader for example)