@Immahnoob @supersid333 @AstolfoCockVore @LoliHat @blueknightfrank it works like this:

Every 3 levels, you can choose a core bonus to add to your mech. It's like a passive ability.
You have all the GMS bonuses available at any time, but the corps also have their own bonuses. To add one of their bonuses to your pool of available bonuses, you need to have 3 levels of license with them (you get one per level).