Binaryhelix101

Ability management displays all the upgradable abilities for your capital ships, they do not have the ability until you select them from the ability management list once you do they appear in the main capital ship menu, the higher the number the greater the benefits, your capital ships can be upgraded to a max level of 10 and have 3 levels of upgrades for the first 3 skills and 1 for the last skill, the ships ultimate, it can be upgraded in any order.

How far away are these planets from your capital? The further away it is the less allegiance you will get. The wiki post on culture gives you a guide to how much allegiance a planet looses. So shift your capital to about the center of your control to increase allegiance to more planets. For the Novalith Cannon check that its not in cool down, its on autocast after construction and check the amount of antimatter it has