If you try using direct admin with different domain, they create different "direct admin" account.
When you have different hosting account, you don't have the permission to access the directory of another account.
So to use JMS with Direct Admin, you have to change the server permission to allow sharing the folders between several hosting account.

In addition, you may also encounter problem with the files and folder permission.
This may be partially solved when suPHP is installed on the server.

Configuration of permission with DirectAdmin is not easy and is not related to JMS.
This is hosting configuration to give the permission between different account.

If you are using JMS with slave site defined in a subdirectory, this should avoid the permission problem.

thank you for the reply. I have it working now following "sitehosters" reply. I now use one and the same hosting account, thus using one subdirectory multisites, which seem to work just fine. DNS settings redirect seperate domains to one single master domain, all is fine in that respect.