is to first draw it on a sheet of paper. Put yourself at the top, and then construct a tree diagram. In my office we use this method to design complex website navigation systems, although we use software to do the drawings.
The idea is obvioulsy to be able to drill down to a document in the shortest number of mouse clicks, and that often means splitting document types into sections of their own, rather than keeping all client files together in one directory. For instance, it may be better to create a folder called 'quotations', and have sub-directories within it, one for each client name (or number), rather than put each client's quoation documents in with other doc types in one client folder.
When you search for a document for a client called 'Jones manufacturing' you already know what it is you're looking for, and if it's a quotation it's probably quicker to go to 'Quotations' and click on 'Jones' than it is to go to 'Clients/Jones/docs/quotation
I hope I've made that understandable - I assure you it works very well. Inside each sub-folder you can have others: 2007 say, and 2008, so everything is filed under a year, or even a month.
To sum up - it can be easier to keep each client's documents by content type, rather than lumping them all under one roof.