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Normally a ROS "project" is a single version-controlled repository that might be just one package but could also be several packages. Often it also has source dependencies that need to be built in the same workspace but are outside of the project repository. It looks like you will be reusing bits from the turtlebot3 repository, so you should keep that as a separate repository, alongside your own underneath the workspace src/ directory. You should not attempt to make a workspace with nested packages.
Your question in written somewhat vaguely, so it's not fully clear what level of advice you're looking for. If you'd like to elaborate about specific things you're not sure about, we can go into more detail then.
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