In my games Command Branch officers do the following: Commanding Officer, Executive Officer, Helm Officers – the obvious, additionally: Judge Advocate Officers, Intelligence Administration Officers, First Contact Specialists, Diplomatic Attaches, Strategic Operations Officers, Fleet Liaison Officers, Crisis Response Team Leaders / Rapid Response Team Leaders. The junior officers – Midshipman, Ensigns, typically serve as Yeoman, Department Administration Coordinators (assisting Department and Division heads with their administration duties on larger vessels) and Deck and/or Watch officers as well as Quartermasters, and Supply/Logistics officers.
As for Enlisted:
Administration Specialist: Administration Specialists serve as Yeoman to senior command officers, administrative assistants to Department Heads of other branches on larger ships or facilities, and make up the bulk of the personnel at major command and coordination facilities such as those that support Fleet Admirals, the Joint Chiefs and Starfleet Liaison offices.
Diplomatic Technician: Primarily serving in support roles for Diplomatic officers and First Contact missions, Diplomatic Technicians prepare briefs for diplomatic and contact missions; prepare and maintain portfolios on diplomatic missions and specific individuals; and serve as mission specialists to support missions where a Diplomatic Officer or Ambassador is unavailable.
Logistics Specialist: These crewmen function in place of or in support of a Logistic Officer. Their duties include procurement and disbursement; managing storage of supplies; and banking and currency exchange operations when necessary.
Paralegal Specialist: These crewmen work exclusively under the JAG department handling support work for the JAG Officers. Sometimes they are sent to brief other departments about developing situations or coordinate between JAG officers and Security Operations.
Personnel Specialist: These crewmen focus on maintaining individual service records, facilitate services for dependents or attached civilians, proctor exams and requests for advanced training school placement, and act as trainers and cadre at programs such as the Academy.
On top of that, I have the senior NCO aboard the vessel put on a Red Shirt and go under the title Chief of the Boat, regardless of their branch of origin. Hope that helps!