I have finally reached Lt Cmd and I am unable to get the additoinal skill level added to the B.O.. I can add a new skill only if I erase the old skill. I am trtying to add a Lt skill the Science officer on a science vessel.
Your Bo's come with skills already for all the levels. If you want to add a different skill than the one they came with you will have to replace the old skill with the new one. If you are trying to use the skill on your ship make sure you have promoted the bo (need to have spent so many points training him to promote him) and make sure the bo is in the Lt station under assignments.
With all the new ships, is there any ship that allows full CDR abilities at all stations?
no, and I doubt you will ever see that. Equal rank slots across the board would defeat the purpose of the main difference between the different classes.
You can have all commander boffs on the ground though. They will use all of their abilities, making them far more effective then lower rank boffs. And of course boffs are not restricted to certain marks of gear at certain ranks, they can equip any gear that your captain can use.