At the moment Business Process Flow assignment is arbitrary with the one at the top being used by default. There should be an option to assign a flow to a record based upon a data attribute. For example, you have a type field in a table, based upon the value of the type field you can assign/re-assign a business process flow. This way if you can have different processes based upon say an Opportunity or Case type without having to resort to code, which is tricky to maintain.