Simone, a couple of thoughts:
In collecting, go through everything. If there are large areas, rooms, garages, etc. that you know you need to go through, but that you don't want to collect and process right now, write it on a piece of paper ("Collect and process storage room") and put that in your inbox. When you get to the processing stage, you'll decide (probably) that this is a project, which means that you'll either park it as a someday/maybe, or you'll identify and record the next action to move it forward. The benefit to this is getting all of those thoughts, obligations, want-to, have-to, shoulds off of your mind and into your system that you trust holds all of your commitments.
Whenever I have something to file in general reference, I ask myself, "why would I need this?" and "where would I look for this when I need it?" That almost always helps me to label things. And yes, be ok with putting one piece of paper in a folder.
And make sure that you're not filing actionable, or possibly actionable, stuff there. If a thing or piece of paper relates to an action, keep it separate from your general reference (in project support).