It appears that Site A is the master account and Sites B & C are "addon" domains which enable access via Site A's subdirectories.
The simple way around this problem is to add mod_rewrite code to Site A which redirects the subdirectory requests (to Sites B & C) to their fully qualified domains, i.e.,
# BEFORE your custom CMS mod_rewrite code and after your RewriteEngine on
RewriteRule ^subdirectoryB/(.*)$ http://www.SiteB/$1 [R=301,L]
RewriteRule ^subdirectoryC/(.*)$ http://www.SiteC/$1 [R=301,L]
I'm sure that, with your level of expertise (if you've created your own CMS) that you can replace subdirectoryB and subdirectoryA as well as SiteB and SiteC with the correct subdirectories and correct domain names.
There are problems within the Apache board so I included this simple mod_rewrite code here rather than there.