So in space I moved the capital ship and now ships crash into it how can I fix it?

You can make invisible lines that bots in ships will follow (but I never learned that)
I think you can do something cheap like put a really big barrier around the capitol ships that only block "flyer" type entities.

Flyer splines are better, and not that hard to do. I recommend reading the tutorial in the ModTools documentation called FlyerSplineFollowing.txt.

I'v taken a look at that txt document and I am completely lost on what to even do when it comes to that, all my ships go out so far then loop around smashing into the side of the capital ship or into the hanger where they crash into the back wall.

@wagromph: A quick peek inside the FAQ would've provided you with this handy tutorial: http://www.gametoast.com/viewtopic.php?p=278511#p278511