Domain URL's for main blog are not retained

I have installed multi domain and have set up a sererate blog for a seperate domain and the URL for that domain. This is working ok first time and the only issue was the URL was showing the subdirectory with the main Domain also showing. Ticking primary solved this issue and the calling domain URL is now constant in the address bar

I also have a couple of domains that I just want to use the main blog/site but I want the calling URL of the domain name to remain constant in the address bar At the moment it is switching to the main site domain URL.