regarding spacing: There is an right click option if you select multiple tools to align or distribute both horizontally and vertically. Every year at inspire this seems to get a big reaction in the 'tips and tricks' sessions, as if it's somehow a new feature. I guess people never look.
As far as documentation goes, within our department we do two main things:
Annotate each tool (when applicable). This helps explain the rationale, and is no different than comment lines in any set of SQL/python/R code. I've used my own commentary when looking at workflows I've developed months prior to remind me why i did something.
Use the Workflow Meta Info. Provide a description of what the intent of the workflow is intended to do, and any other relevant notes.
The reason we chose this option over containers is that moving things around seemed to be easier this way, and the comment boxes just seemed to make things cluttered.
