There are many ways to do so.
My preferred way is to make the documents in DevonThink available to other projects by means of a big unstructured indexed ‘interface’ folder (similar to the ‘sync DT with Goodreader’ folder suggested in this post: A better way to use MobileSync with GoodReader?).
I replicate the entries of files in DevonThink that I want to make available to other applications to the interface group, move them to the external folder, and put aliases to them in my project folders.
I recommend collapsing the interface group in DT’s outline and excluding it from classify, search and see also.
This isn’t very complicated, provided that you never replicate an entry with an arrow icon behind its name (that icon says: ‘this entry is already in an indexed group’) to an indexed group and you never rename, add or delete files in the interface folder by any other means than DevonThink.
Weblocation files referring to a group in DevonThink provide an even easier way to ‘interface’ DevonThink with project folders in the finder:
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Replicate (or move) entries of all the documents relevant to a certain project to one group in DevonThink or create a smart group that collects all the relevant documents
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Select this group in DevonThink and choose ‘Copy item link’ from the contextual menu (this copies a link to this group to the clipboard)
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Paste the link in a text document or window (it doesn’t matter where, an OS X sticky, a ‘post a reply’ window in Safari, a note in DevonThink, a Word file you happen to be working on)
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Select this link and drag it to the relevant project folder in the Finder (this creates a weblocation file in that folder)
When you double click on this weblocation file the corresponding group opens in DevonThink.