I also use my own numbers to identify my source documentation. Years ago when I began my research, I started with number 1 and entered that number in my notes. Now that I have PAF 4, I am in the process of entering these documents into the sources and deleting them from my notes. I began by inputting into the title field #0001 - then the title of my source. If I had entered my document #1 without the zeroes, when I got to #10, PAF put it order after #1!! This is the only way that I could figure out to do it to keep them in numerical order in PAF. If your numbering system has letters and/or dashes, I'm not sure what sequence PAF will put them into.
I hope this helps you out a little. Sorry I couldn't answer your other questions.