There are a number of ways that you can apply an automatic layout to your diagrams.
Using the auto-layout modal in the diagram editor
Clicking the button in the diagram editor will open the auto-layout modal. This allows you to choose the implementation, and to customise the various properties that are used when applying the algorithm. Diagram elements are still movable manually after running auto-layout, and you still need to save the workspace using the "Save workspace" button.
You will need to install Graphviz on your server if using the on-premises installation.
Using the Java client library (before uploading the workspace)
If you're creating your software architecture using the Structurizr for Java client library, you can apply the Graphviz automatic layout algorithm before uploading the workspace to Structurizr. See Graphviz automatic layout for more details.