Great question!
There are many ways to do this, I’d say the most common one is probably to store the bitrise.yml in your repository. You can also store it in a separate repository and use that as a submodule for example in your main repo, just make sure that the same SSH key can be used for all the repos during the build.
For storing the bitrise.yml in your repository, you can find a guide here: http://devcenter.bitrise.io/tips-and-tricks/use-bitrise-yml-from-repository/
Right now the main disadvantage of this approach is the lack of UI editor, but that will soon change - we’re working on a complete revision of the workflow editor and it will be open source, and you will be able to run it locally on your Mac too, editing any bitrise.yml from your Mac directly. Related #dev:work-in-progress discussion: Workflow Editor “v2” (Open Source & Offline Workflow Editor)
The first beta is scheduled for this week, if you’re interested make sure to subscribe to/watch this discussion.
If anyone have any additional solution for this, please share it with us here!