Thanks for the help dfhfhUUAA–, I really appreciate. I think I prefer to have:
/public_html/.htaccess selecting WordPress as domain.com
/public_html/phpsite/.htaccess? + custom php site as domain.com/phpsite
One last thing. What do you think about installing WordPress automatically with Softaculous apps in Cpanel? Will Softaculous wordpress get my site on mydomain.com considering this situation?