I feel the same way. My manual is written to our service requiments and not in ISO format. It's organized better, flows better, and is more user friendly.
HOWEVER, in order to make it through our annual audits, I had to develop what turned out to be a three-column, 19-page, cross reference grid to reference where to go in my 22-page Quality Manual to find our ISO elements.
And, quite frankly, I'm getting a little tired of maintaining those two documents, so I am probably going to bite the bullet and re-do the QM into ISO order later this year. Should be LOTS of fun!