As of now, there is not a way to manage distributed git repos from a single Track & Plan project in an integrated fashion. It can be done manually, but you would need to link to commits in the remote repos in a given work item.
This can be done through the Links tab of any given work item and using the Add SVN Revisions or Add Related Artefacts. This would allow you to link to the remote repos (whether in IDS, GitHub, or private SCM tooling), while still leveraging Track & Plan as an overall planning repo.
Some of this is due to the way projects are constructed in IBM Bluemix DevOps Services today. A single project has the notion of a single git repo, a single Track & Plan instance, and a single Build Pipeline. Some of these requirements are expanding, but the platform provides integration capabilities to work with your code the way you need to right now. For example, project owners can build from remote GitHub repos in the project's Build Pipeline, so that code can be managed as you see fit, but built and deployed on IBM Bluemix.