Hey, though the comments on here appear to be several years old, I would like to provide the correct answer to the question, for anyone else who happens upon this page as I did.

"Blow the man down" refers to taking down the main sail of a ship. It was a big job requiring several hands who all had to work in unison. The purpose of the song was to provide a rhythm to keep them in sync. Any song could be used and the words often changed. It was the rhythm that mattered.