Does it matter that he is assigned to a station or not?
On my vice admiral engineer I removed my efficient BO from his station and replaced it with a normal BO and all ship power levels remained the same.On my lt commander sci(he is efficient captain) I get +1 engine/shield/aux if I use my efficient saurian in the science station instead of a normal BO.This is a bit confusing.
I ask this because it is not nevermind that I buy a few engineer saurians for 29 mill./1 or I buy tacticals for 49 mill.(the current price).
Yes, as said above, the Saurian does need to be assigned to a position on your ship to see a difference.
A BO with the Efficient trait, such as a Saurian or a Borg "Amazon" (C-Store) BO, gives only a +5 to each of the four Efficiency skills, each of those affecting their specific subsystem when set below 75, being most effective closer to 25. Also, the game rounds the display, but it does keep the fractional amounts for computing things like weapon damage, engine speed, BO powers, etc. So while you only saw a +1 on your Sci Captain, the Engineer Captain would still have received a small boost too.
For more details, take a look at my Ship Power Calculator, linked in my signature. You can see/test how having one or more Efficient BO (yes they are stackable with themselves and an Efficient Captain) would affect your powers, before you spend your millions of credits.