Primary Domain for Domain Mapper

I am not sure if this has been discussed, and a search yielded very little results, so I am going to go out on a limb here. I have the Domain Mapping plugin working perfectly, so far as the plugin is designed to work anyhow. I checked out the updated version of doncha's work today, which has been modified to allow a primary blog, but from what I have seen, it still only supports installations using subdomain blogs. How can I hack this feature of making a primary domain for my blog? Some of my blogs have 2 or 3 domains each, and it redirects each domain independently to the same blog using different URL's, which if I understand correctly is not good for SEO results, because there are multiple domains for one site.

Now that I have rambled, perhaps someone could help me integrate this into the plugin with a quick (or not so quick) fix, perhaps even helping along an upgrade to include this as-is.