I’d go by divisions, so I would count in command/operations/science. As a rule of thumb, I’d say it’s 20/40/40 on each ship, maybe 25/45/35. Within the science personnel, I’d say numbers lean about 70/30 in favour of scientific personnel over medical personnel. Btw. there’s a list on Command Division Jobs other than ordering people around and flying shuttles.
If you like it a bit more complicated and/or take the ship’s class and mission profile into account, I’d say to simply look at the ship’s stats. Calculate on basis of the department numbers. Each point of any department is 100 / total department points in %.
Or you combine the methods and distribute one half of the crew by the first and the other half by the latter. 