I'm not sure what I have to offer is correct or practical. But I keep my 'important' papers in 3-hole binders and use the archival safe clear sheet protectors. The papers that are of legal size do stick up above the binder but as long as my binders are in tall shelves, it's no problem. I keep the scanned copies of those longer papers with the originals and do bend those over to fit the sheet protectors. Some of my less important papers I have in a file cabinet in file folders. I go through those once in a while & eventually decide I don't need them, and they get tossed. Of course there are researchers out there who think we don't need any paper at all. But, we all have original documents and papers that need to be kept.
Good luck with whatever you end up doing!