One of the most confusing yet simple things about Fleets is the order of the Ships in the Fleet. Due to the way combat works the first ship in the fleet list is the first to take damage from alien encounters. In that light one wants to put the screening ships at the front of the ship list and the more important vessels at or near the rear of the ship list. For building a fleet from scratch ships are added to the front of the ship list as they are built. So for instance if you build 5 ships of DD class and name them DD with the starting number of 1 then the ship list will look like so: DD5, DD4, DD3, DD2, DD1. If the ships are all of the same class probably not too big a deal. But if you have some valuable ships such as your transports they should be at the rear of the fleet not leading the charge. Therefore it is wise to build all your important ships first followed by the screening ships. Then if your fleet runs into unexpected hostile fleets or planets the screening ships take damage first and the ships at the rear may never take any damage or maybe very little.
Now if you're transferring ships from one fleet to another it's important to know the order the ships will be added to the new fleet.
If you're using Action Code 135, Multiple Ship Transfer, that transfers one or more of a particular class of ship (build code) from a fleet to another fleet, the ships go to the front of the new fleet. However if you are merging one entire fleet, Action Code 25, into another then the ships go to the back of the new fleet.
Why is this important. For one thing you don't want your brand new very expensive shiny new carrier at the front of the fleet, nor do you want those fully loaded transports leading the charge into the next battle. So if you have a fleet that you need to merge with another fleet it's important to remember where the ships go in the ship list.
A good way of getting all ships in the proper position from one fleet to another when the first fleet is a mixed list of ships is to:
First use Action Code 135 to transfer all the screening ships to the front of the ship list in the new fleet. Note this might take several actions if you have several different ship classes that need to move to the new fleet.
Then use Action Code 25 to merge the remaining important ships to the back of the ship list in the new fleet.
Now you know.