I would say that you should develop your system based on your company's unique situation. Don't be forced into a certain way of doing something by a software package.
My advice is to stay as simple as possible with everything in the QMS. Not only will it make your certification process easier, but people will also get more benefit out of it that way. For example, keep the quality manual as short as possible and don't duplicate the standard.
Working with a good consultant to create an implementation plan might be more effective for you vs buying software.