Well, I thought I was making progress, merged the two sites onto the same folder level. Both sites use configuration.php, so I merged the file, got errors because a variable was already defined. No problem, put them in two files, and included them with include_once, seemd to solve the problem. Then I got a database error, when I tried to include any of the root files (clientarea.php) from a folder within the cms. So I thought, I'll move the configuration data to the directory that's calling it. Seemed to work, but then the script boots me to a directory below my working directory.
Seems like you've done everything in your power to disable any script including the whmcs encrypted base files. Might be good for keeping the hackers out, but as a paying customer I find it very annoying, my final attempt is to try and build the cms structure around the whmcs files, instead of pointing/including them with a component i've written.
Any help is appreciated