Dear Amy,
No, that's the opposite of what I thought I said!
You keep the text in the order that it appears in the manuscript, and you put the modern verse numbers before the relevant portion of text.
So, if a manuscript has John 1:4 before 1:3, the transcription should look like this:
1:1 ΒΆ In the beginning was the Word,
and the Word was with God, and the
Word was God. 1:2 He was in the beginning
with God. 1:4 In him was life, and the life
was the light of all people. 1:3 All things
came into being through him, and without
him not one thing came into being that
has come into being. 1:5 The light shines
in the darkness, and the darkness did not
overcome it.
Hope that helps!
Hugh