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I have two web-sites with yola, I can't seem to publish both of them, is the primary setting part of my confusion ? and if so will both sites come up in the search engines if i choose just one of them for the primary one.
Primary sites refer to a situation where you publish one site under two domains. This for example could be mysite.com and mysite.yolasite.com.
Often people start out with a sub-domain and when they are happy with this they then decide to purchase a custom domain. Meanwhile a following has taken hold with their sub-domain and they don't wish to lose this group or the site ranking that may have evolved. In this case you would then publish to both domains concurrently. The general concensus is to set your primary site as being the custom domain and the secondary as your sub-domain. In effect if a user goes to your sub-domain they will be immediately and seamlessly directed to your custom domain.
If you have two or more discrete web-sites then you don't set one as a primary and other(s) as sub-ordinate. They are different entities completely as they have different content.
If you have other issues with publishing please post the details here and someone will help for sure.