I had been wondering how to do this myself. I could not find it in the documentation. However, after a little experimenting, I discovered, that the "Run Project" runs the Process Flows in the ORDER IN WHICH THEY APPEAR in the Project Tree.
If I rearrange the order in the project tree (drag-n-drop), then it changes the order they run in with the "run project" action.
This worked in EGuide 4.3. As I could not find it documented, my only concern is that the behavior might change without notice in a future version.