Workflow is very flexible and can handle very complex processes. That said, it is easy to become overwhelmed if you aren't careful.

For your business process, rather than thinking of it as one big, complex workflow, break it into smaller pieces and think about how those pieces will interact. Most of our complex workflows are actually smaller, simpler workflows invoked by one "master workflow", using input and output parameters in the child workflows. That way, making changes to the individual pieces becomes easy, since the only thing you care about are their inputs and outputs (rather than their implementation details). This also makes it easy to reason about everything.

Take the BPM I and Capture Workflow CPPs if you haven't already. There's also at least one white paper and several conference course slides on the Support Site that covers Workflow diagramming and design.