WORF just ruled on this this morning... points are attached to the ship. (just like Fleet Captain, so makes sense)
-The Fleet Commander resource is assigned to the ship it is affecting and counts against the 50 point limit for that ship.
-If a Captain assigned to your ship is discarded or moved to another ship, immediately discard the Fleet Commander resource and decrease your hull or shields (whichever you selected to increase with the resource) by one.
-When building your fleet, the Captain with the highest printed Skill Number is your Primary Captain. If two or more of the Captains have the same printed Skill Number, you must choose one to be the Primary Captain for the entire game. When any card, including this one, affects your Captain, it must affect the Primary Captain first.
-If an Admiral or any card that may replace your captain is assigned to your ship and one of your two Captains is discarded or disabled, the Admiral or card does not become a Captain. Admirals or card that may replace captains only become a Captain if there are no other Captains on your ship.
-Borg Drone tokens are only assigned to the primary Captain (the highest printed skill) when building your fleet. Your secondary Captain may not gain Borg Drone Tokens.
-Please note, Gareb and the Romulan Drone Pilot may not be assigned by this card.