Drowning in Articles

I am a year and a half into my PhD and am coming to the end of writing my background chapter.  For an archaeologist, this means writing about the historical context of my research and the current state of knowledge about the time period.  I have been tackling this in thematic chunks and my material has been organized in these sections.  Now I'm starting to integrate these sections by writing the more specific contextual sections and I'm finding that my filing system is starting to break down.  I'm spending too much time trying to find a particular article as stuff is spread across the themes.

I think I need to reorganize my articles and take a close inventory of what I have and where it is.  I use EndNote and am very diligent about entering reference information.  I would like to try keeping better track of where each article is in my system and whether I have printed it off or if I've moved it into a thematic collection for some purpose. 

I think the best system for me to adopt will be an alphabetical system by the first author's last name.  I have avoided this in the past since often sets of authors write together multiple times about similar things but alternate who the first author is.  This can make it difficult to keep track of all resources on a particular topic, but clearly keeping things by topic is no longer working.  I guess I'll have to give it a try and give myself permission to redo it if it isn't better.

Now, I have a filing cabinet in my office in the department that I can use, but I intend to work from home when I move in June.  At that point, I will need to devise a filing system to use there, but in the mean time, I can use the hanging files in my office.

I guess I will be spreading my paper out on the floor sometime soon and alphabetizing and cross-referencing it in EndNote.  I'll be sure to take some pictures of the before, during, and after and keep you updated on the progress.

How do other people keep track of articles and resources?