I just plugged the guitar into one of XLR/line combo inputs. The vocal was the X/Y mic (replaced with the stereo shotgun mic module). The guitar was the next free input. In iPad interface mode, the H6 combines the X/Y mic and the four extra inputs to a stereo pair.
Your H4N Pro does the same thing, but the X/Y mic head isn't replaceable and there are only two combo ins. Just use the X/Y mic a little closer and plug your guitar in at the bottom.
That or you could just use a mic into one input and your guitar into the other.
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