Instructions for use of Apparatus : One or more box /files or lever-arch files are suitable for these. If you have more than one set of instructions for a particular piece of apparatus you must decide whether to file them all in the same file, create a back-up file with the spares or throw them away.
Alphabetical order is as good a way to file them as any other. You could file them according to manufacturer/supplier wise and then in alphabetical order. It is a good idea to keep guarantees and service or maintenance agreements with the instructions, although you could create special files for these. There is also a case to be made out for keeping guarantees with the instructions. The alternative is to create a special file for guarantees. The same can be said for service/maintenance agreements. Either file them with the instructions for use of the apparatus to which they refer or create a file specially for service/maintenance agreements.