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>    I'm a gnubie.  Is there a simple guide restricted to correct compiler use
> (command-line syntax etc.)?

http://www.delorie.com/djgpp/doc/ug/

> If not, someone should write a thorough one, just a thought.

http://www.delorie.com/gnu/docs/gcc/gcc_toc.html

> Also, should I put new include files in that directory?

You should put include files in the same directory as the sources.
The compiler knows to look for them there.