With the changes to fighters in v2.6, there is going to be quite a lot of docking and undocking of parasite ships. Therefore when you split a fleet or detach single units, any ships (including fighters) in the new fleet(s) that are currently in a hangar are automatically undocked if their mothership is not part of their new fleet. As with v2.5, if you move a mothership into a new fleet, any docked ships go with it.
For example, the CV Ark Royal has twelve Eagle fighters on board. If you select three of those fighters on the Organization tab and select Split TG, those three fighters will automatically undock and form a new fleet. If instead you detached the Ark Royal from its fleet, all twelve fighters would transfer with it.
Already in v2.5 is the ability for a fleet to launch all parasite ships, although they will remain within the same fleet, plus the ability to recover all ships in the same location to any assigned motherships within the current fleet.
New for v2.6 is the Squadron window. This allows you to create Squadrons, which function as adminstrative units. When a squadron is selected, the squadron name, nickname, number of fighters in the squadron, average grade and the most senior pilot are displayed. Below is a list of all fighters in the squadron with details of the fighter name, class, squadron, current fleet, assigned mothership, current location (which is a mothership or system) and grade. You can also show all fighters for that race, which is why Squadron is one of the columns.
You can assign any fighter to any squadron, creating mixed squadrons if desired and transfer fighters between squadrons as required. You can also use this window to assign fighters to motherships. The squadron itself doesn't have a physical location as it is an adminstrative grouping of fighters. However, you can launch and recover fighters by squadron and mothership using this window. If a squadron and a mothership are selected, clicking Launch will create a new fleet with the name of the squadron (e.g. "VFA-01 Wild Tigers") and any fighters from that squadron on the selected mothership will be undocked and moved into that fleet. Clicking recover will dock all fighters in the currently selected squadron assigned to the currently selected mothership.
In addition to this, the Ship window also allows you to set an assigned mothership, launch from your current mothership, land on your assigned mothership, release all parasites if you are a mothership and recover all parasites that have you as assigned mothership.
I hope that all of these various options will provide enough flexibility to manage parasites and motherships without too much trouble.
Steve