Learning ubuntu:
Click the link "linuxcommands" in my sig for a starting point. You can also read the Ubuntu Pocket Guide (it was written for an older version 8.04, but most of the non-configuration entries are the same)
To access the server from a remote location you'll want to use ssh (tons of info through this forum or google on setting up ssh)
Your program has its own documentation on its website.
Here is an older serverguide for Ubuntu 6.10 server. There is probably a new one out there, I just didn't spend much time looking for one.
As always, Google can help you answer or find just about anything.
EDIT: here is the new server guide for 10.04
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