I think chords come out quite well.  I don't think you can change the fret number as this is showing which position on the fretboard you are in.  It would be good to have the facility to create a document with just the chord library you've created for teaching new chords etc.

I agree the chords look great.  But you are showing the problem I described.  The fret number should indicate 5 and should be to the left of the D note on the 5th string.
 
Don't most guitarists think the bass note's position = the fret number in a chord diagram?

I'm used to them with the first finger position shown.  Sometimes it's done in roman numerals.  The main thing is for it to be clear for the reader.  It can be done different ways though.  Have a look at something like Mike Di Liddo's 60 Contemporary Voicings in the Aebersold Jazz Books.  Perhaps some more editing options for chords might be in a future version.

If I can't figure where to play by the shape and name, I put my guitar away and play the harmonica for a while
 
Seriously, I haven't assumed a particular standard for this and I honestly can't tell how it's done in most TAB books or other software.
 
 

Michael A.D.
 The fret number should indicate 5 and should be to the left of the D note on the 5th string.
 
Don't most guitarists think the bass note's position = the fret number in a chord diagram?

Sorry I disagree with you on both, IMHO that only confuses things for beginners.
Number stating bottom fret of chord is nice and simple.
If you want to indicate Root, 3rd, 5th, etc. - roman numerals, colors or even shapes are techniques I've seen used.
GP7 sounds interesting... from what I understand it can't now but if it could indicate note type at some point that would rock.