If you use the sync with external folder feature to edit your Scriv project as plain text files in another editor – in my case iA Writer on the iPad – and want to add annotations, simply enclose the text you wish to annotate in double brackets, thus:
((annotation example here))
When next opening the project in Scrivener, this text magically appears in a red annotation bubble.
Bob’s yer uncle.
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Martin Sketchley 