Keeping track of multiple sites, multiple templates and even multiple use cases, as with the NYCROPHONE Shop, takes a lot of effort but SourceTree and Git make the whole process immensely easier.
As shown in the image, NYCROPHONE has a repository for each major template for the site, including the two blogs and our staging sites. Some of this could be combined into branches but since the Git setup is also publishing to the live sites on commit, it really helps to keep everything totally separate.