So - this is the current rule with respect to naval combat prior to amphibious invasions:
Transports carrying cargo that will be conducting an amphibious assault that move into a sea zone with enemy surface combat naval units must wait until the naval battle has been resolved before disembarking cargo from that sea zone. The attacking player may attack with some of his naval units and reserve others to support the amphibious assault by conducting shore bombardment. Naval units may not both conduct naval combat and support the amphibious assault.
For battles where the defender has only air units attacking an enemy naval amphibious invasion force, only one round of air to ship combat is fought against naval units before transport disembark their cargo onto the beaches. Air units may continue to attack naval units on subsequent rounds of combat, but their cargo is considered disembarked after the first round.
Transports that are returned during sub movement interdiction, naval combat or the first round of air to ship combat may not disembark their cargo and remain in the sea zone with their cargo (they may be retreated out of the combat sea zone per the normal retreat rules at the end of the combat round).