I posted the question to the Atlassian board as well and got an answer I think I like the best:
Jason Monsorno · 762 karma · Aug 30 '13 at 04:38 PM
Deployment projects in Bamboo seem to be dependant on the existance of an artifact, the catch is you don't necessary need to use that artifact so you could use an empty artifact and do completely independent steps. Deployment projects are still fairly new to Bamboo and your structure may favor the "normal" workflow so each environment would be a separate manual stage.
The Deployment project do have a separate workflow and versioning. To use Deployment projects in your scenario, I'd suggest making the artifact the entire checkout then each Deployment environment can build a copy of the artifact. The space-saving/less-time-efficient option would be to just save the current revision in a file as the artifact and use that to check it out and build in each Deployment environment.