After you have done the initial installation of the operating system, you shouldn't need to use the VMware console. Most of your work should be done by connecting to your server with SSH.
Software
If you are using Linux or a Mac, you should have the ssh command-line tool installed. Instructions below assume this.
On Windows, you can use PuTTY or the Windows SSH Client. On CSIL Windows machines, you will find the SSH Client at Start → Programs → SSH Secure Shell → Secure File Transfer Client.
SSH (Command-Line) Connections
You cannot connect directly from the outside Internet to your project machine. To work remotely, you will have to first connect to the course server, cmpt470.csil.sfu.ca:
ssh userid@cmpt470.csil.sfu.ca
You can then connect to your project machine:
ssh userid@mxn
You should be able to tunnel X-Windows across both connections if you have xauth installed on your server (apt-get install xauth). You may have to add a -X switch to the ssh commands to get it working.
You should be able to do most of the work you need to do on the server at the command line this way.
Transferring Files
The two-step connection to the server will make it difficult to transfer files to your group's machine. This shouldn't be much of a problem since you shouldn't need SCP to get your code to the server.
In general, you should use your Subversion repository to deploy your code: commit the code you're developing to the repository, SSH to the group's server and checkout/update the directory there.
Software will generally be installed with the Ubuntu package manager (apt-get), not uploaded and installed manually.