I think the Slot option explained in other threats is a good start.

But I experienced quit a lot that when I was on a ground mission, I got msg from my Ship and displayed was a BO with was on the ground mission, so not available on the ship... this shoud be fixed...

and further more, I think I should be able to set position, like "first officer", "second officer" ( one of these two has to stay on the ship while the Captain is on an away mission!)

That's just one of the many funny things about some of the dialogs and randomly generated content. I love when the Borg want the mighty Federation to save them from some thug extortionists. While there isn't really a way to designate a first or second in command in game just yet (at least, not that I know of) you can build your away team at the crew assignments screen and usually via a dialog box as you beam down to the away mission. You could always leave whoever you want to call your first officer behind.