Yes, you can do that; I would personally ship the containers separately and provide minimal orchestration. Why? Because if you bundle multiple containers together, they will run on a single host. And if they run on a single host, it's generally easy enough to craft your own ad hoc orchestration.
But if you have multiple containers that require really weird, specific hoops to run together, it's definitely an option!
Note that future versions of Docker will let you ship and manipulate a group of containers as a single object. Currently this is scheduled for 0.8 (October release).
But if you have multiple containers that require really weird, specific hoops to run together, it's definitely an option!