well my system concept is multilayered. you can control turrets by setting their objectives, targets, and behavior. you can go to the battery level where you control a bunch of turrets manually. then to the individual turret level mostly useful for surgical strikes knocking out a ships engine with a bfgreen for example. most of the weapons you will want to be left on automatic. you can step up or down to the level needed.
a good gui is important here. the way i see it at the top level you should be able to drag ships off the tac map (really an oversized radar with icons (possibly 3d) to represent ships) and onto the target lists for individual turrets or batteries. the turrets would grouped by their general direction, you pick port, starbord, fore, aft, dorsal, or ventral. theese options form a pane. selecting one puts the targeting map into that frame of referance. all the batteries for that direction will be listed in a row next to it, each in its own little pane with its options. you can select a battery and its individual guns would be displayed as a second row under it. so you can quickly get to any battery, any gun, in any direction with no more than 3 clicks. each object has its own target list, which comes up when an object is selected. i figure the whole interface would take up the top 20% of the hud. possibly with side panels and the tac map taking up the rest of the screen for the high level mode. when you put a turret or battery into manual the tac map is minimized and the view changes to the proper frame of referance.
turrets/batteries could be set to agressive, defensive, or disarmed. when you drop to turret or battery mode (by selecting the turret or battery from a list), turrets can only be fired by direct command and aimed by mouse, the agressive/defensive/disarmed option is replaced with ripple fire options. you only can manually fire turrets in battery (or the selected turret), all other turrets use ai behavior depending on the high level settings.