'Design' what you feel will be a 'good' system and an implementation plan. Then get buy-in from everyone and off you go.
It all depends upon how far you want to go. One client a few years back put every manager and supervisor through flow charting courses and they entirely re-did all their documentation. It was an expensive project but it was done during implementation and management supported it. They did it through process mapping.
On the other hand, I did a consultation at a company and found it had, when they underwent implementation back in 1993, started to convert a massive amount of documentation and the effort eventually petered out. By that time they essentially had 2 sets of books, so to speak, which essentially said the same thing - just in different ways. The old stuff was never obsoleted because there was no overall buy in nor would management fully fund the project. The project was almost 3/4 completed when it ground to a halt.
In one company they wanted to simplify. One thing we did was remove the 20+ controlled copies of the quality manual and put the master online (eliminated paper copies all together).
When I want to do something like this I draw up what I want to achieve and draft a project plan. I want to be ready to present 'Now' and 'Proposed' as well as how to get there.
If you're wanting to go through a serious effort to change to flow charts the best way I can recommend is what I recommend to clients: See
http://Elsmar.com/Imp/sld195.htm - read through the process mapping section.
With clients very early I attempt to diagram the documentation system 'as it will be'. There are examples of this in the Flow_Charts.ppt file which is part of the Implementation Guide set of files. An example is
http://Elsmar.com/pdf_files/Doc_Structure.pdf
I try to press clients to embrace flow charts, as most who know me know I'm a flow chart 'nut'.