there are really a few ways to deal with capships in freespace. one way the stick and mouse way, where you fly the ship with the stick and aim some or all the turrets with a mouse. but this sorta misses the entire point of flying a capship. its sorta like a freighter in freelancer, you may have 10 or so turrets at your disposal, but you can only shoot at one thing at a time. capships have a completely different job that a fighter. a fighter's job is usually to intercept things, destroy small things, defend big things, gather intel for big things and generally keep the space clean enough for big things to operate. classicly in freespace the capships are really white elephants. and if you put two ships on the grid without any waypoints they will just shoot at eachother till one blows up. while it doesnt work too well yet, this way is possible now (im on too that bug now. actually it took me 2 days of reading my code to realize i was on to the bug way back when i stopped coding lua to work with c).
now another way is more akin to mechwarrior, beaning its more about tagtics than good aim. you have a ship, with way more guns and armor that one person should be allowed to control. rather than just click, click, kill, kill. you need to manage energy, heat, damage control, all while manuvering into the best position while coordinating with other capships and fighters/bombers to meet the mision objectives. rather than control all guns at once, you micromanage them. you devide the turrets up into batteries and give each one a job to do or take control of the battery yourself if youre not too busy with other tasks. if your mission is to beam the **** out of something, you might want to do the aiming yourself. while you may command something like the flak batteries or the blob turrets or tell the fighters who to kill and how to link their guns, but dealing with small ships really isnt your job, cept giving them orders through their commander. what you need here is a radar which you may interact with. if a bomber wing jumps in you can click on the wing closest to it and have them deal with it. this way is possible, but im nowhere near to that level of talent.