Ok,
So the last reply helped somewhat.
What we do now is using custom skins for each account. This is a bit annoying, because we have to restrict each account with a skin using its branding, but it works.
One thing I did not know that set me back was that if you use the Style-Override (Using styles-tab and entering logo, url etc for the domain), it will override the skin settings.
Now when we leave that empty it works well.
Perhaps this will be useful to anyone with a similar problem.
Also Link on Changing Skins:
ZWC 5.0 Themes