Hey, that is XWindows you are looking at
Xtools sux. Delete it now, XDarwin howver is awasome. If you are running XFree86 your set up fine.
You see, XWindows is what is called a windows server, it contains all the neceissary data for a gui, but requires a separete client program to deliver that GUI. This is where windowing enviroments come in, these are things like KDE and GNOME. The installation procedures for these can be found at
www.fink.com . It is a bit of a pain in the ass. Also, messing with the X stuff is a pretty major adittion to OSX so be carefull and have all your voletile data tucked away in a safe place.
You don't really need to mess with any of that however. If you download some Darwin versions of X software that uses XFree86, things like the GIMP, and AbiWord, you can run these thrugh XWindows with no problem. Just launch the program from the xterminal, or duble click it's icon under OSX (some programs include a dubleclickable icon, some don't).
As far as UNIX commands, a good heavy book, like the O'Rilley book, or even UNIX for dummies is perfect. You will learn the BSD OS, more thrugh tinkering however. So learn the man command and look up "UNIX commands" on google, you will get some basic comands, like ls, ls-1, etc. This is a good way to start, don't be afraid of it, just tinker.
www.resexcelence.com has a great section on Darwin.
If you are interested in running KDE and GNOME, you can do so thrugh t he pure Darwin core. You access this from typeing >console at the login prompt. But don't fuck with that now
your better off getting used to Xfree as a whole.
Another excellent site with resources that may help you is
http://osx.hyperjeff.net/ , he has a great section on XWindows for darwin.
That's about it, keep at it, youll figure it out. It ain't all that hard, granted, Im a newb too
but I learn more every day. I think the bigest hurdle is that some of the UNIX commands are wierd and hard to remember, and yet, they are all pretty short.
Whatever.