References and Scrivener

Pardon the newbie question, but I have been struggling to come up with a good workflow for my non-fiction documents (usually about 5,000 words long), though it would apply for a book length project as well. Does anyone know a great reference manager that can take pdfs and urls off the internet and later let me include the references in either Scrivener or Word?

At the moment, I search the internet in safari or devonagent. When I find a page I want, i clip it with Devonthink pro (because I want it in a serachble database) and also Pinboard (because I want to preserve a copy of the page).Then I take extracts out of these documents and put them in the binder of my Scrivener article. I then write in Scrivener using the references in the binderand transfer to Word for polishing.

What would really help me is to use a reference manager that easily takes urls of webpages and also pdfs that are downloaded from the internet. I have Bookends but find it very complicated and can’t figure how to get an article from the nytimes.com into it. Any other better solutions out there?

Have you tried Zotero? It picks up metadata from most major databases or from doi nr. It has a Word plugin.

Just one word: Sente

Papers

I have used BibDesk all these years. It works well with a LaTeX/Scrivener workflow since you can define your own export templates. I use my MultiMarkdown template for that:
gist.github.com/DivineDominion/6870769

It’s looks pretty similar to Bookends, though. If you share what exactly you’re experiencing problems with, I’d love to see how the problem could be solved because I’d like to see how well BibDesk performs for other people.