Why it matters
A workflow of sixty tools with default names is unreadable a month later, including by the person who built it. Alteryx is a visual tool, so the layout is the documentation.
Tool containers
Select several tools, right-click, Add To New Container. Give it a name describing the stage — Load and clean sales, Join to product master, Write outputs.
Containers collapse, which turns sixty tools into six readable blocks.
They can also be disabled, which skips everything inside on the next run. That is the fastest way to test one branch without deleting anything.
Annotations
Each tool has an annotation field in its configuration. Filled in, it displays on the canvas.
Write why, not what. "Filter" is visible already; "Exclude internal test accounts" is the thing someone needs to know.
Comments and layout
The Comment tool adds free text or a coloured box behind a section. Use it for headers and for anything a future reader will need explained.
Beyond that: keep the flow left to right, align tools, and avoid crossing connections. All three take seconds and make a genuine difference to how quickly the workflow can be understood.
Documenting the workflow
The workflow's own Configuration properties hold a name, description and author. Worth filling in — it appears in the Gallery listing and is often the only clue about ownership when something breaks a year later.