That's a short question with a long answer 😉 Before you go do anything, work out how you want to use your Workareas: Do you want a separate Workarea per target system (to keep things organized) or one for all systems? (It is typically a play-off between security and re-usability). Then if you use Web Assistant you'll probably want a separate Workarea for the help content (again, possibly by system).
For a Workarea that is (primarily) used for learning content, how you organize everything under Root is up to you. Some Master Authors like to set up separate 'Development' and 'Final' (Publishing) Groups, but as publishing is controlled by the Status I personally don't tend to do this. But I do have one high-level Group per project/organization/system (basically anything that warrants its own Trainer). Below the 'entry point' to your Trainer (in your 'Final' Group), organize everything the way you want your users to see it. If you have a Glossary you probably want to put this within your 'organization' Group but outside the 'Trainer entry point' Group so it doesn't appear in the Trainer outline. Similarly for other 'reference-only' content.
Always have a Toolbox that contains your Templates, common assets (like shared images), etc.. You can keep this and all its contents checked out if you want to stop Authors from being able to change the content.
For Workareas used (only) for Web Assistant help, things are a bit different. I personally never look in there and just let all the help content build up in Unsorted, but some Master Authors like to keep this organized by moving to Groups under Root organized by application/version/language.
Anyone else want to add to this, with their best practices?
Bluesky
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