What you describe doesn't sound like the best way to present 'the meat' of the document. Putting all of your notes at the bottom of the page separates it from the reference. Instead, I would use a side by side layout where the ancient text is on one side of the page and your content sits beside it.

Your choices would then be to do this with:

1. a two column section page setup;
2. a two column table; or
3. a one column layout with a huge margin on one side and lots of floating frames or shapes sitting in that margin area

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Andrew Lockton
Chrysalis Design, Melbourne Australia