I'm not a prolific shooter and shoot 35mm B&W with a small amount of 2 1/4X 2 1/4. I file my negatives in archival plastic sleeves in 3 ring notebooks. Each roll is numbered and dated in succession. I place the contact sheet (when I bother to make one) and a sheet of notes of the film development with each sheet of negatives. I use sticky notes next to each negative I've printed with a reference which to which pages in a notebook I use when printing. I've found it confusing referring to the printing book so when I get the time I will make a sheet for each printed negative showing times,filtering,dodging,etc and place it in the notebook. So if I want to reprint a negative I just go to the negative book and the printing info is there next to the negative.
As far as the prints. When I print I usually try to get 3 or 4 decent prints of each negative in a session. (After toning, drydown,etc I'm lucky if I get 1 or 2 prints I'm happy with). I dry mount the two best. One goes into a portfolio box, one goes into a backup portfolio. The other 1 or 2 goes into an empty paper box. That is where I'm the most disorganized. I have only been printing a little over a year and can see myself in a few years with boxes of prints with no rhyme or reason.