Now I see the distinction between your "in" box and your "pending" box. Personally, I use a drawer in my desk for that. The desk drawer to my immediate left is one of those deep ones. In it I keep my tickler file. I use 1 - 31 tabbed manila dividers (rather than an accordian file). Behind that I have A - Z lettered tabbed manila dividers. When I come across a piece of paper that gives rise to a project and which I'll need for one or more of the NA's on that project, I create a folder for the project, labelled with the project name and place that physical paper into it, then file it alphabetically in the drawer.
This is not part of my office's general reference filing. And if I worked at home, I think I would still try to keep it separate from my home general reference filing.
As an alternative, if the NA on the item is fairly self-evident, and I know exactly when I want to deal with it, I just toss it into the tickler section and deal with it on the appropriate day.