If you are just looking for the key to come out right, punch the chords in (shape wise, i.e. if you play a C shape with the capo, enter a C) as if at the nut, then transpose up 6 semitones to get the key to match. If you are trying to get the Guitar fretboard in BIAB to display correctly you will have to go the routes as noted above.
Apologies if this is too far off base of what you want and/or a bit too simple but I don't know what level of BIAB experience you have.
Good luck.