ONLY use one of the "Fleet Formation Mods" at a time during a game session.

NOTE: You can switch between the Fleet Formation Mods that display the vanilla ship trails and the Fleet Formation Mods that specifically eliminate vanilla ships trails.
The versions can be swapped at any time during a game (this will require you to save and restart the client). There are no adverse effects in doing this.

You can also vary which Fleet Formation Mod you use during different points in the game. This includes switching between the mods to change ship distances in a formation;
For example early on with smaller ships you could use "Fleet Formation Mod v3.0" (the ships are closer together) and when ships are large use "Fleet Formation Mod v2" (the ships are more spread out).

If you use mods that rescale ships (Such as Downscale Ships) or any Solar system scale mods, then you have to use the Fleet Formation mods specific to scale changes. The non-scaled mods will not function correctly with rescaled ships and solar systems.

However you can use "Fleet Formation Mod - Downscaled" (the ships show the trails) and at any time switch to the "Fleet Formation Mod - No Trails Downscaled" (the ships do not show the trails).

Because of the scale changes the scaling mods are not interchangeable and you cannot swap them, except for as described above. Those mods are:

Fleet Formation Mod - Downscaled
Fleet Formation Mod - No Trails Downscaled
Fleet Formation Mod (Downscaled Ships & Solar System Scale)
Fleet Formation Mod (For Solar System Scale Changes)
Fleet Formation Mod for Real Space - Ships in Scaling