I have the following setup
Primary Domain = http://www.company.com
Add on domain = http://www.companyhome.com = subdirectory
WordPress has been installed in the add-on domain with the following settings:
WP URL = http://www.comapnyname.com/subdirectory
Home URL = http://www.companyhome.com
Everything seems to work EXCEPT anything that wants wo modify the Worpress htaccess file is actually trying to modify the ROOT htaccess file instead of the one under the subdirectory. This is not correct, you are supposed to be able to have the two URL's defined differently. If I make the WP url match it in fact works again. I am convinced there is something needed in one or both of the htacess files but I am not sure what. I have tried everything. I need a wordpress guru to make this right so I can admin through SSL on the primary domain yet allow regular access through the home URL.