Workspaces are basically a way to switch between active work streams and configurations. For example, I can be working on a feature branch of a project and I'm asked to quickly fix a bug in the same branch, but without my new changes - or to stop working on that feature and fix a bug in a release branch. Using multiple workspaces are just one way to achieve that quickly.
Effectively, you can think of a workspace as a local repository of code; all the changes I do in there are local to that workspace.
If you have two unrelated projects, then I don't believe that maintaining two separate workspaces will give you any advantage. This article goes into more depth; but my advice would be that if you're not familiar with TFS then try using it without multiple workspaces until you come to an issue that having multiple workspaces will solve for you.