"I'm not sure how to set up my projects. When should I create a folder, and when should I create a new workspace?"
Think of a workspace as the top level of your workflow. Each workspace can have multiple subfolders, but all members of the workspace will have access to its subfolders.
If you work with different teams for different projects, set up a workspace for each project and invite only that project's team members to the workspaces.
For more information about structuring workspaces and some example structures, please see Structuring Workspaces.