Hmmm, If you're alone on the bridge this is the cause of your probs. The usual stock method for maning the the guns is to ask your watch officer (who would normally be standing beside you) to tell the crew to man their stations (done by clicking on the characters actual manifest form, automated controll is then initiated. If you want to controll the gun yourself, you must first man it (as above) and then climb down to it and click the guns' 'halo'.
If you're alone up there, then this is obviously impossible, so where are your crew? I'm wondering, have you succesfully completed the intro/tutorial?
Try disabling all your mods and then see if you have the same prob, would def recomend clompleting at least one patrol with no mods so you know what position normal is and can identify what has been changed by your mods.