There's some good info on organizing in the classic "Getting Things Done" by David Allen. But, it is a real slog - not an easy read. It's a bit out of date for email and stuff, but I was able to glean some good habits from it.
I learned some things that I applied to me electronic "paperwork" - my email box and notes/tasks etc. at work. These I've stuck with for a couple years now. Just like you're saying with papers, I keep a zero inbox now. I don't use the inbox as a to-do list, because things just get lost. Basically as it comes in it's filed for action with a reminder set, done right away, filed for later reference, or my favorite - deleted! Like that pile of papers, an inbox with hundreds of items just drains the will to do anything whenever you see it.
I even bought a special set of files that fit in a desktop sized file hanger that works as a "tickler" file list - it has slots for each month that can be rotated forward so things can be filed for action and then attended to as the month comes up. Anyway, I gave up on that. 99% of my paperwork for personal life is online now, too.
Anyway, a good book to at least read thru, even if it doesn't all stick.
