Yes, you can create links that open on a specific notebook of your repo. The directory hierarchy you set up in the repo will be respected so the relative path to any other file and directory remains. The notebook opens with it location in the path as the working directory. There even is an absolute path; however, I suspect from helping you with another question, you wouldn’t want to use that as you intend your notebooks to be used via multiple serving avenues so you inherit the early parts of the absolute path from the providing resource.
The MyBinder.org page, where you can launch and get pasteable text for links or badges, let’s you specify a Path to a notebook file as you are filling out the form. You can then use the URL it generates. It follows a pattern where the path to the specific notebook relative the main directory follows ?filepath=.
(Note if you are using the JupyterLab 1.0 or greater interface you need to look into workspaces.)