I may be misunderstanding the game entirely, but I think different BOs have different abilities, and you are not able to change them.
For space abilities, though, if you have multiple consoles.. say you have 2 engineering consoles available on your ship, then whatever Engineer BO you stick in that double console spot will be able to use 2 abilities. And as such, you will gain more abilities as you gain access to better ships with more consoles and/or BO slots.
What I am talking about is each has a set of abilities, which show up in the ui of that BO, problem I am having is I cant change those abilities out, if that BO has 3 slot(commanders ships have 3 slot for abilities for tactical officers on a escort ship), when I upgrade to a higher rank, it over rights whatever is in next slot, so I have rank 1, rank 2, rank 3, etc, instead of just the highest rank of that ability, then 2 other abilities.
I know how to upgrade the abilities, I dont know how to access the new abilities, or place them where i want. For example, to rank up Fire at Will 1 it will tell me I have to overwrite another ability, and then will place it in the next slot on the ui, so 1 and 2 are up.
Seriously, this ui is garbage, and not to have an ability ui for your BO to access the abilities they is friggen retarded. Should have a pull down menu with everything they can do. You would think with the huge success of WoW, someone would have paid attention to its ui....
All your seated Boffs' abilities show up on the power trays immediately when they're seated. They have to be seated in an appropriate station to use Space abilities. I.E., if it's a Lieutenant ability, the Boff has to be at least Lieutenant in rank, and seated in at least a Lieutenant boff station. If you want to move a power around in the trays, you can open the Powers window, or right-click and drag.
Ground abilities automatically show by their entry in the Team listing, and have the same rank requirements.
All Boffs have two skills at each rank, one for space and one for ground. Yes, to give them new abilities in a given rank, you have to replace old ones.