There are lots of good textbooks and tutorials on using various flavours of UNIX (e.g. HPC) and Linux. 

The slightly un-good news (for people who aren't "power users") is that you probably need to understand the basics of using the command shell if you are using a "stock" NeCTAR Linux image on your virtual.  (They typically have a "server" install rather than a "desktop" install to save disc space.)

And the good news is that once you have learned the basics of the UNIX shell and the core commands, they are pretty must the same for all flavours.  (Indeed, there are even official standards.  Google for POSIX ...) And what is more, the UNIX shell and commands work together much better that Windows batch scripts.

(But if you really prefer a graphical user interface, then you can have one.  Just install the packages and connect using VNC or SSH with X11 forwarding.)

UNIX / Linux Introductions and Tutorials

As I mentioned above, there are lots of good one, but here are a couple that would probably suit "busy researchers".

Linux Manuals / Documentation sites

Forums and Q&A sites

... for when you really need to ask a question.

Training and Workshops

The Software Carpentery group run a series of "on-site" workshops called "Bootcamps" offering free introductory training on a variety of IT topics.  Check their schedule of upcoming events here.