I find it most helpful to put information into Evernote, and projects and next actions into my list manager (currently Toodledo). In Evernote, I have some notebooks
Project and Next Action Support
Stuff moves from Inbox to Support, and then to Done or Reference. I have other, specialized notebooks, and some stuff goes directly to Reference, but that's the flow of work. Done is for stuff I think I won't need to see again, Reference for stuff I think I might. Evernote search lets me not agonize over which notebook stuff goes into. I use tags to keep support information together, but will move the material out of Support and delete the tag after a project is clearly finished.
Example: I need to send a number of letters of recommendation for a student to various places (web sites these days). Each email I get is clipped into the Inbox. When I process it, it gets tagged and put in Support. When I'm working on this student's recommendations, I'll look at Support items with the right tag. When I process each request (filling out a web form and uploading a letter), I move that item from Support to Done. In a few months, I'll delete the tag, but still be able to find all the information by search on the student's name.
Working on the project and doing the next actions is driven by my lists, not by Evernote.
Hope this helps!