I was actually emailing with one of the core developers (Fabian Jakobs) of Clound9 IDE having some basic questions, so here are the answers:
1. How do I commit the code back to github?
You need to clone from a read/write github url (starting with git@). After cloning you are asked to upload your cloud9 public key to github. Afterwards you can use command line git from the console at the bottom of the page.
2. I am also running the local version, and have not figure out a way to open a project/load my own code from a directory.
The local server supports a bunch of command line arguments. With "-w" you can specify a workspace directory. With "-l" you specify the host cloud9 is listening on. By default it can only be accessed from localhost.