I read this as a posting from over last year, but did it ever come to pass, and if so, how do I set it up?
Department Heads and First Officers
Subsequent to the duty roster system going live we will be rolling out the next component of the system: Department Heads and your First Officer.
Bridge officers will be able to "eat" duty officers of their own branch to learn those duty officer's passive abilities. (Fictionally, think of it as the duty officers are joining that bridge officer's staff.)
With the appropriate expenditures of Merit/Honor and for bridge officers with adequate training, a player can appoint a bridge officer to head up one of six departments - Tactical, Security, Science, Medical, Engineering, Operations. Once heading up a department, those "eaten" duty officer skills will become active.
(For the record, the term "eaten" is used in this description to make sure it is clear that the duty officer goes away.)
Slotting between stations (the current "Assignment" tab), away team and department head slots are independent; if you slot a bridge officer into the Tactical Department Head slot, their passive powers will be in effect. That exact same bridge officer could also be slotted into a bridge station or away team, but whether that bridge officer is or isn't his or her department passives will be in effect.
From department heads, a bridge officer can be promoted to a First Officer once you acquire special "trainer" duty officers. The skill imparted to a First Officer, however, will be an active, clickable skill that you can slot on your power bar and use in space.
When you appoint a first officer, another BO can replace them as department head. Your first officer's passive duty officer skills will however still be active as a first officer - so this means you can effectively double up on the passives in one department.
First Officers may be demoted, but there will be an associated cost, probably in Merit/Honor. The former first officer's skills will be retained, although inert unless reinstated. This is also true of department heads who are removed from their position - the passives they ate from their duty officers will still be there, they just will be inert and inactive until they are reinstated. The first officer skills have not been designed yet, but they are currently envisioned as being new skills, probably similar to your captain skills.
Department head and first officer skills for bridge officers will be in addition to their existing skills - getting them to play nicely with the bridge officers' existing skills is one of the reasons why that part of the system will be rolled out after the duty officer part of the system.
Department head skills are taken from duty officers in their own branch, so the passive skills they gain will in fact be associated with their branch of service. First officer active powers will probably also fall into this pattern as well, but there is still a lot of design that has to be done in this area so I can't promise anything.
Integral to the introduction of department heads and your First Officer we will be revisiting the entire crew user interface in an effort to streamline and integrate it, all with an eye to allowing us to build even more deeply upon that to provide even more functionality and depth to your crew.
This didn't, but the timeline being talked about last time anything was said regarding it hasn't come to pass yet (that is, S7+ - S7 has been stated to have a new personal advancement system, but not confirmed to be department heads yet).
There was one change worth noting: Shortly before he left and Borticus and a couple others inherited his systems, Heretic did say that the first officer power was being changed - instead of unique new powers it would be one player power, commander or lower, from either a different career path than your captain, or a second instance of one from your career path. Still, Season 7 is optimistically around December-February, and few things survive through the testing phase, let alone from the design boards.