Naval units can not attack land units and land units can not attack sea units.
Land units on board transports can not fire. If the transport is sunk, the cargo is destroyed too.
If an attacker wishes to launch an amphibious assault, and there are defending naval units in the seazone adjacent to the target land zone, then there is first a naval battle involving the naval units only. If the attacking navy survives, then it may unload the land units from its transports, and the land battle ensues. If the attacker has any battleships, they get a single support shot at 4 into the land battle. The battleship is immune to attack from defenders in the land battle.
Planes and bombers are airunits. They can participate in the sea battle or the land battle, but not both. The sea zone and land zone are completely separate areas. So move the planes into the seazone to participate in the naval battle, or move them to the land zone to participate in the land battle. Just make sure they have enough movemnet points to get back to friendly territory during the non-combat phase.
If all the factory pieces are used up, no more factories can be built.
This is the same for all pieces in the game. It limits the number of separate units of that type each army can have. For example, each player has only 2 battleships. So at most each player can have 2 fleets with battleships in the game at one time. You can use the read and white chips to create 2 stacks of battleships, but you are always limited to 2 stacks.
I hope this helps. Welcome to the game. I think its one of the best around.