The key to this is to provide a system that you, as owner of the business process, can understand. And we do this by letting you build your own, entire system. First thing, therefore, is simply to sketch out how your system connects together - the parts involved and how they relate to each other.
Not as complicated as you might be worrying about. Simply draw out on a piece of paper how the business process works - not the business flow diagram at this point, simply the principal things and how they connect to each other. Here's a typical Business / Object Model;
Object Modeller is the unique tool that lets you build and manage the various objects that comprise your business process, as sketched out above. Not only does it let you build the objects, it also lets you create the associations between them, together with the forms that you can then use to add / edit / control the objects.
Now you have your object types built, you can add as many of these objects and edit them all via your website, either through the back end administration interface OR via custom forms through the front of the website.