Organizing collections and subcollections

I've been using Zotero for a while now, but now I'm starting to use if for a large new research project for the first time. In past projects (pre-Zotero) I have found it useful to separate printed primary, archival, and secondary sources, and am thinking about the best way to do this in Zotero. So far I've created a project collection, with subcollections for primary and secondary sources. I've seen discussion on here about primary and secondary bibliographies, but not about initial strategy for collecting. Also I'm curious about how people find the notes feature for taking verbatim notes on non-digitized records.
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