Some questions that came up:
1.) Can a ship fire its guns overtop of a friendly and/or enemy ship?
2.) Can you target a more distant hex of a ship?
1. Yes. Ships do not block the ability to shoot at a target in any way (the only exception is the Screening rules found in the Commander's Manual, where a player may spend X amount of MPs to specifically move a ship to block a shot).
2. Yes. Page 13 of the Lieutenant's Manual, under Determining Range, where it states "...and follow the shortest path to the target...", the "target' is referring to the hex you're attempting to hit. i.e. the reason it says "target" and not "ship" is that a ship occupies multiple hexes and provided that you follow all the appropriate rules for determining firing arcs, range and determining damage arcs, you choose which hex occupied by the target ship you're attempting to attack.
Randall