So, it sounds like you have PuTTY worked out, but just not sure how to go about navigating in the *nix world. Check this link for a list of basic commands:
Unix commands reference card
Here are a few main ones to get started on.
ls - List directory
cd dirname - Change directory to dirname
rm thisfile - Remove file called thisfile
mv thisfile thatfile - Move thisfile to thatfile (rename)
cp thisfile thatfile - Copy thisfile to thatfile
cat thisfile - View contents of thisfile
more thisfile - View contents of thisfile, page-by-page (spacebar advances pages)
file thisfile - find out what kind of file "thisfile" is. (ASCII text, binary, etc)
pwd - Show your current directory location
That's a start, anyway

Good luck!