My recommendation, don't start with any OS specific guide. You need to first learn the design of the Unix command line. Read section #1 of Eric Raymond's book
here. Then, in no particular order start to learn how you can pass input in and out of programs via piping, redirection, etc. Learn Unix permissions, the file system layout of a traditional Unix system, etc. Once you start to understand the basics of the overall Unix design, then picking up OS specifics will be trivial. Since I know Unix, it isn't hard for me to adjust to using a BSD, Solaris, Linux, OS X, or anything else. This would be much much harder if the design of a Unix system was completely foreign to you.
Since there is much to learn here it would also help to share with us your goals so that perhaps we can help you come up with a project to apply all of this stuff.