I was wondering if I need to factor in the crop factor in the focal length when using an APS-C camera...
ie. using a Canon 6D with a 200mm fullframe lens vs. a Canon 80D (crop factor 1,6) with the same 200mm fullframe lens. So does Ekos / Astroberry automatically know from the different sensorsizes that it needs to recalculate the FOV or do I need to create a separate lens with 320mm if i am using a fullframe lens on a APS-C camera? and if I have to create a second lens does the f stop change as well since the lens is the same I would not think so...
No. FOV is determined with focal length and sensor specs. The whole crop factor thing only applies to photographers trying to match an FOV in relation to a standard film dimension. The concept doesn't apply to astrophotography.