I use EndNote for recording references and bibliographic details, and type my research notes into the Endnote research note field for that reference (I also add a pdf of journal articles etc in the figures field). This way I can save a research note with a page or pinpoint reference, and the research note is always attached to that reference. An added bonus is that the entire database can be backed up regularly to avoid future heartache.
But there’s more, I am using Scrivener to write ‘scraps’ and chapters; these can be sorted a bit like index cards and then eventually exported to Word as a final document.
In Scrivener, there is a research folder to which you can drag documents for ease of reference when working on your scraps/chapters.
Experimenting with Endnote this morning, I find I can easily export a single reference with its bibliographic details and all of the content of the research notes field to a text or RTF document. This document can then be dragged to the research folder in Scrivener, so you can easily switch between the research note and the scrap on which you are working.
The method: In Endnote, finish working on the reference and close the reference. Select the reference in the list of references in the main window. Go to File > Export > Type in a unique name for the export file > Select the location to save the file (I use Desktop) > Save as Text Only or RTF > in Output Style, select ‘Show All Fields’ > make sure the ‘Export Selected References’ checkbox is checked > Click ‘Save’. A text document or RTF document will save to your desktop.
I am also using Evernote to save internet pages and info – those items can be sorted and filed in Evernote, and then exported from Evernote as a document to be dragged into the research folder in Scrivener.
Of course, annotated PDF documents can also be dragged into the Scrivener research folder, together with other media such as audio and movie files.