Whats your rank? I assume your Lt Commander as your promoting your BO's to Lt. Ok so heres how it works, when you promote your BO to Lt they gain access to a second skill. However to use that skill they would need to be put in a Lt BO station on your ship. Bridge officers only have access to skills at the level of the station they are in.
So if you had a tier 2 cruiser for example. You would have 3 Ensign stations and 1 Lt station (engineering). So I put an engineer, a science and a tactical BO in each of the ensign stations. They all have access to their first skill only. I then put another engineer in the Lt station. The BO in that Lt station will have access to his second skill.
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So if you had a tier 2 cruiser for example. You would have 3 Ensign stations and 1 Lt station (engineering). So I put an engineer, a science and a tactical BO in each of the ensign stations. They all have access to their first skill only. I then put another engineer in the Lt station. The BO in that Lt station will have access to his second skill.
Make sense?