Unless there's a way im unaware of the only way to work on a project with another person at the same time is to use the same account, then once someone has finished something have one the other copy his work down then save and have the other refresh his/her page.
Yes, we know this is inadequate. We're still kind of in putting-out-fires mode, but support for classes is the next thing on our list (actually meeting tomorrow to plan things out) and joint ownership of projects will be on that list.
Something we're doing often is sharing sprites. If two students are both working on a project they can export sprites and import them into each other's version of the project.