You can track projects on GitHub Enterprise by creating milestones with associated issues and pull requests.
About milestones
You can use milestones to track a project's progress over time.
Creating and editing milestones for issues and pull requests
You can create a milestone to track a project's progress over time.
Associating milestones with issues and pull requests
You can associate similar issues and pull requests with a milestone to better track their progress.
Filtering issues and pull requests by milestone
Issues and pull requests can be filtered based on the milestone they're associated with. Once you've associated an issue or pull request with a milestone, you can find items based on their milestones.
Viewing your milestone's progress
In order to track your project's milestones, you'll want to get a better understanding of how many open issues and pull requests are remaining.