"Also, the box is only blue if there is an OPEN (aka un-used) port. Clicking a closed blue box dissmounts the item, freeing up the port. This is usefull if you don't like the ballance of colors or the way your guns look on your ships. You can un-mount and re-mount in a different order to make it look pimpin'."
Also good advice! Without knowing this, I played through the whole story line and up to about level 30. Let me tell you, I would have enjoyed having my missles located in "adjacent" ports (which they sometimes were). And of course, it would have been nice to have some aesthetic balance to my weapon configuration!
Thanks again, Tom.