I think you first need to determine the true or actual pitch of the notes. Obviously, you want the notes in the right places. Guitars have a huge range, so you really do need the treble/bass staff. So, when you have determined the true pitches, choose a treble/bass cutoff that results in the cleanest look.
Another option is to use two separate staves, one for treble and one for bass. Then you can put the notes where you want them, bass notes on the bass clef, treble on the treble clef, without having to worry about a cutoff, which unnaturally forces the notes to one or the other staves.
Of course, there are those few notes that fall between the two clefs, Bb, B, C, Db and D ( or A#, B, C,and C#, if you are in a sharp key). They can go where you want them, on either clef. I make the decision based on rhythmic groupings. It makes more sense to keep B or Bb on the bass clef if it's part of a group of 8th notes, or a tuplet figure.
Also, if for some reason the notes are incorrectly placed on either staff - for example, notes which belong on the treble clef are erroneously placed on the bass clef - use the transpose feature to bring them up an octave to where they belong.