I have somewhat fixed it I think but am unsure if this is the right way.
I disabled the primary domain check so all domains will work on the selected blogs.
My thought was, for other websites with multiple domains in this network I can set a primary domain in my server settings aswell (just redirect non-site domains in the server-admin with a 301 redirect to the domain of choise (eg.. primary domain).
I would like an expert opinion on this sollution because I'm unsure if this will give the right results (also for SEO).