I would suggest you try one of the scripts in these threads as a starting point:
QuoteHighlight&Annotate script
The scripts in that thread allow you to add multiple annotations from a single document into a single document. There are scripts to do this with both an rtf file and an omni outliner file.
Annotation Pane (Annotation with Links, Notes, Tags v3)
The script in that thread allows you to add to multiple annotations from a single document and stores them as single notes in a linked group rather than in a single file.
Questions about them should be asked in the threads dealing with them.
There are other scripts in the forum that do variations on this theme.
Frederiko