It would have been listed like... Identification #: _____2001___. Keep in mind that here at our shop we are only dealing with D1.1 and not ASME. I think the K.I.S.S. method is the best way to handle them. Our system was already started when I moved into this office, so I went with what was already in place. Ours start with number 1 and go on up, without any real attempt to keep the processes in any particular order. After I started adding to the file, I did keep the SMAW WPS of the same joint configuration with the FCAW WPS right behind it of that same joint. These are the two primary welding methods used in our shop (no GMAW or GTAW and rarely any SAW).
For example: joint designation B-U4b -prequalified
SMAW is listed as Identification #:___21___
FCAW is listed as Identification #:___22___
I also placed the joint designation directly above the page number on the lower right corner of the page just to make it easy to find when flipping through the pages.
When we get audited, I didn't want our welders to feel nervous, fumbling around trying to look up a procedure for an auditor that might be auditing our shop.
Any numbering system is acceptable, just use something that works for you and your welders.