I have promoted all of my BOs to Lt and started putting points in their skills but they aren't showing up in the list of available skills to transfer to the task bar. Is there some trick that I'm missing? Do they not show up until i get them to a certain rank? Thanks in advanced for help.
If that's the case you need to have a look at the assignments tab. You will see that depending on the class of ship you have, you will have varying rank bridge officer positions. So for instance, a Lt. Cdr cruiser has (I think, without looking it up) 1 ensign tactical slot, 1 ensign science slot, 1 ensign engineer slot and 1 Lieutenant engineer slot.
So although you have promoted your boffs to Lt., you will find that only one of them has access to the Lt. Powers in space - that's the game mechanic, it limits the available powers you have and forces you to make tough decisions. Ground powers will work fine though for promoted officers.
Higher tier ships will have more available higher level slots, but you won't find a ship where you could have all your boffs at the same skill rank.