How to use domain mapping

MGx.com is now on a dedicated server and I have full access to root and admin and I am the only user - just my domains. MGx is using subdomain multisite installs and I was able to install domain mapping so that it worked but I had not "mapped" anything.
Now I want to add thezuchini.com to the multisite network or at thezuchini.mgx.com. The domain already resolves to the server and I created a new site in admin for thezuchini as well as an A record for thezuchini.mgx.com. and mapped thezuchini.com to thezuchini.mgx.com and now everything is a mess and I had to comment out sunrise and rename the plugin folder in order to access the main site - everything went to thezuchini.com/blogs/blogs.dir-a or something like that and finished with a 404 error.
Even after deleting the site if I reenable domain_mapping I go back to the 404 page. How do I fix this?
Thanks