I've moved the thread; if anything to do with DirectAdmin at all it's a user-level question.
The copy of .htaccess in the cgi-bin directly is there to keep contents of cgi-bin files to be visible as files and/or directories rather than just showing the output.
If you need an .htaccess file for some other purpose, you do it the same with DirectAdmin as with any other hosting control panel. If you need help with .htaccess files you can google your question.
Jeff