There's no one right way to handle physical documents, except the one that's right for you. You'll have to determine for yourself how you need to be reminded of actions involving such materials. That may require some trial-and-error.
Since that's high-level and abstract, let me give you a concrete example based on my own experience. When I first implemented GTD, I dedicated one of my stacking trays for actionable hardcopy documents. I thought it would be redundant to add them to my next actions list in my digital list organizer, so I did not. What I found was that I would forget to check the tray with the actionable documents, and when I did I would struggle in some cases to remember what the hell some of those documents were and what the action related to them was. So I would have to re-process and re-decide about many of these documents every time I engaged with the stack. Obviously, that's not workable. So I began adding these things the appropriate action list (which for me was "at office" for stuff at the office and "at home" for the stuff at home -- my roles are pretty easy to manage so my system is not rocket science) and found this solution much easier.
Based on a suggestion in an online article or blog post authored by Kelly Forrister, I dedicated yet another of my stacking trays to magazines and other "nice-to-read" documents. I treat that as a "read/review" tray. What distinguishes these from the actionable documents tray is that if I don't get to read/reviews before they go stale (like a current events magazine that gets so old it's no longer worth reading) there's no real harm done; I can just recycle them.
So there you have it, right. Based on what bcmyers2112 and Kelly Forrister say, this is the way to handle it. Problem solved.
No. Not so fast.
@ggray50's suggestion is just as valid. If you find it easier to use the physical document as your primary reminder, you might resist putting them in your next actions list. It might create the kind of friction that causes you to resist using your system. In that case, it would make more sense to have a stacking tray (or something like that) to hold all physical documents that are actionable, whether those are documents related to a project or magazines you want to read. You many not even need (or want) to segregate important documents from casual reading.
It all depends on how your mind works, as well as the nature of your profession and lifestyle.
@Oogiem's system is similar to mine but much more elaborate; then again, she is a farmer with activities that take place in multiple locations throughout her farming operation. The simplicity of my system is likely inadequate for her needs; her system is almost certainly more elaborate than would benefit me.
At some point before this thread runs its course someone might come up with yet another valid suggestion. I'd suggest keeping your mind open to what is suggested, but let your experience be the actual guide for choosing a solution.
