You should have weapon computer selected when you are building the cannons, that is how they auto-link. You can do it afterwards easily, by selecting the computer with C, and then point the cannons with mouse and Shift+V 2 or 3 times until you see them all glow purple.
You shouldn\'t cover the core, it is the most recommended way to get in. I haven\'t tested much, but you can put a build block on your ship, and if you can get to fly the ship through it, i don\'t know. Entering through weapons computer won\'t let you fly. Entering through turret or docked ship with Down (or was it Up?) key works, but it disables Bobby AI for turrets. Also you can\'t have turrets on if you dock your ship to station. You cannot use arrow keys movement to turrets through station\'s build block.
