When I work with Nintex Workflow ( version 2010 in Internet explore 11) and need to edit a function box in the lower part of a workflow, I need to scroll to the top of the workflow to see the edit-box. Why is that ?
I'm assuming you mean the workflow setting button. The issue you are seeing is because the Nintex menu sits within SharePoint ribbon and we all know Microsoft is not about to put a floating ribbon on SharePoint.
If this is not what you were referring to, a screenshot may help. Also, if your workflow is extremely long, try adding a few action sets and combining several actions within that. You can easily collapse the action set which helps you see more parts of your workflow at once if you have to scroll.