For help about documenting your code I recommend reading phpDocumentor's manual
Example generating documentation on the command line:
./phpdocumentor/phpdoc -d './phpdocumentor' -t '/var/www/html/docs/' -o HTML:Smarty/Evolve:default -s on
This will put the documentation in /var/www/html/docs, uses the Evolve template and also includes the source code.
It might be a noob question, but how can I install this template in my phpDocumentor?