In ILINX Capture, the most basic unit is a batch profile. A batch profile is a container that includes batch fields, one or more document types and a workflow. It is unique, self-contained and completely independent from each other. In general, you would want to create a batch profile for each unique workflow process in the system.
If you have multiple doc types that mostly follow the same process, you should think about creating a single batch profile to hold all the doc types. With this setup, you can then use permissions to give users access to their specific doc types. Furthermore, within the workflow designer you want to break your workflow logic into common processes, shared by all doc types and specific doc type sub-flows. If you find that you need to create too many sub-flows, re-evaluate the relationship between a batch and doc types and see if you can fix the problem.
The goal is to create unique workflow processes so that system maintenance is easy; and one way to deal with that is to avoid duplicating batch profiles that are performing the same tasks.