I think most people new to SC have this question, I know I did at one point.
If you need to make edits to your theme, when running your extension development environment locally, you need to first fetch the current active theme. Run gulp extension:fetch without selecting any extensions. This will download the current active theme into the Workspace/Extras folder. This will allow you to run gulp extension:local and make edits to the theme templates/sass. You just have to remember to copy all changes to your theme development environment. Once you have finished with theme edits, deploy and activate your theme via the theme development environment. Then, again, fetch the theme via the extension development environment.
I have found it is helpful, perhaps best practice, to fetch the current activate theme when developing an extension. Also, helpful to fetch your extensions when developing the theme.
Hope this helps