I assume you mean that the manuals are both [Skill name] 2? The convention seems to be that green manuals are Lieutenant rank skills, blue manuals are Lt. Commander rank, and purple manuals are Commander rank. Certain skills have level 1 at Ensign, others have it at Lieutenant or Lt. Commander. So Tactical Team 2 is green (Lieutenant), Cannon: Rapid Fire is blue (Lt. Commander), and Gravity Well 2 is purple (Commander).
They have up to 4 skills. First slot takes ensign level skills, second slot Lieutenant level and so on. You can't put skills of a different rank (read level) in a different slot. Starship bridge stations work the same way.
Bridge officers do not lose skills when they're promoted. They can have up to 4 ground skills and 4 space skills active at one time (Ensigns have 1 skill on each side, and gain one slot per rank, so Commanders have 4).
Just to confuse you a bit more, Boffs can have "reserve" skills that are trained but not active. These skills can be swapped in from either their skill tab on the status screen or the Stations tab, though I think you have to be in sector space or a social hub like ESD, just like changing your captain's traits.
Comments
http://www.arcgames.com/en/games/star-trek-online/news/detail/10142423-star-trek-online-console-differences
What specific skill manuals are you looking at?
Just to confuse you a bit more, Boffs can have "reserve" skills that are trained but not active. These skills can be swapped in from either their skill tab on the status screen or the Stations tab, though I think you have to be in sector space or a social hub like ESD, just like changing your captain's traits.