Your question was already answered in your other post (which asked the same question).
If they are in a console position that doesnt allow for Tier2 skills they wont be able to use them. (Except for ground skills)
Check your assignment window to see which ones you have available.
You seemed confused by this response and I'm not sure why as it is a solid answer. Did you even bother looking at your assignment window like he suggested? The beginner ship has 3 ensign consoles (1 of each type). The T2 ship has 1 additional Lieutenant console (the type depends on the class of ship you pick). Your T2 BO abilities only work when they are placed on Lieutenant (T2) consoles.