Is there a way to transpose individual parts, like transpose only the guitar a third up, so I have the correct chords, when I use the capo.
Have you tried adding an independent key signature to that staff? I’ve never tried it, but I think it would work. You would select only that key signature to transpose.
EDIT: tried it, it works. One caveat: if C is your original key, enter C in the popover, close it using Alt-Enter. Then to transpose, you have to select not only the range of notes, but also the C major signpost.