1.  There is no easy way to do this as there is no trigger option of "Ships sunk" as there is for aircraft kills or ground targets destroyed.   Also you didn't state whether you want the player to destroy two of the ships or any friendly aircraft.  Here are a couple of options I use depending on the mission:

    a) If you use infrastructure ships instead of moving ships then you can select the trigger "Ground targets destroyed".  Infrastructure ships are considered ground targets in the game.  Now when the player destroys any two of the infrastructure ships the goals will be met.  If the player sinks a moving ship it will not count toward the goal.  On the other hand, if the player misses all of the ships but destroys two water towers the goals are still met since the water towers are also considered to be ground targets.

    b)In missions where I want two moving ships sunk I usually pick out three or four logical target ships and set triggers/events around them.  I then stack a few events together into different combinations and set goals around them.  For example, if I have an 8 ship convoy I might randomly choose ships A,B,C,D to be sunk.  Then stack event combinations such as A & B or C & D; A & C or B & D, etc.  I won't use all of the possible combinations because there are just too many but I try to get enough so that there ia a good chance of meeting the goal of sinking two ships.  I use hidden goals attached to these different combinations.  If a hidden goal is not met it doesn't count against the player.  If you didn't use hidden goals you would have to sink every combination of ships you entered to meet the goals.  Since the goals are attached to the ships and not the player the goals can be met if the wingmen sink any of the right combinations.  The burden doesn't fall entirely on the player.  Recognize that when using this method more than two ships may need to be sunk to actually reach the goals written into the mission.
   
Neither method is perfect but they work within the limits of the Mission Builder.  

2.  Set you mission type for the bombers to either "Strike", "Anti-ship", "Search & Destroy" or "CAS".  Then be sure to set a waypoint close to or directly on top of the object you want atacked. Now you can choose one of the attack options under "Action" for that wayoint.  I'm not sure which tutorial you were refering to but I cover setting up a Strike mission in the "Raid on Tarawa" section of my tutorial.  Remember that "Anti-ship" is used for moving ships.  When attacking infrastructure ships use the "Strike" mission option.  Also, level bombers will not track a moving ship the way a torpedo or dive bomber will.  That means if you are trying to bomb a comvoy of moving ships with a flight of B-24's you need to set your attack waypoint at the spot where you think the ships will be when you drop the bombs.  A little tricky.

The "Raid on Tarawa" mission shows how to set up an attack mission, not specifically one for AI planes, although the principle is the same.

By what you are saying I am assuming that you want your AI flight of dive bombers to hit a ship.  If it is a moving ship then set your mission type to "Anti-ship".  When you plot the wayoints select your attack waypoint as "Attack w/bombs".  Once you do that  the waypoint marker will change to a triangle.  Move the triangle until it is directly on top of the ship icon (or the ships waypoint marker closest to the point where you want the attack to occur).  Once the triangle is directly over the ship's icon or waypoint you will see the name of the ship as the target under where you selected "Attack w/bombs".  You may need to zoom in to get the placement right.  If you are not exactly on top of the ship your target will read "current point".  Once you have the attack marker positioned properly you can finish your mission editing.  The dive bombers will track the moving ship and drop their bombs on the ship.  Dive bombers and torpedo bombers will track a moving ship, level bombers won't.

If you want your dive bombers to hit infrastructure ships then select "Strike" as the mission type.  Set up your attack waypoint and place the triangle on top of the target as described above.