Powers all go in certain spots. For example tractor beam 1 is always an ensign level power. If you want tractor beam 2, that is always a LT level power. You can't put tractor beam 2 or 3 into an ensign level slot, they will only go into LT and LTC slots respectively.
The only exceptions are some high level powers, where the level 2 and 3 versions are both for commander level BO slots.
And this isn't logical. Why if I get pefection in one skill a can't change it for the same skil, but lower level? Ie. if i can jam sensor I i can't upgrade it to level III?
I think it should be chaneged.