huh?
i don't really know what's your problem.
you can have two configs, or even more, that's not a problem.
though nxing won't do the rewrites that are in the .htaccess files, since they are made normally for apache.
For nxing you have to specify the rewrites in the config of the site.
If the rewrites don't collide with existing code, you can put them in one config-file.
if you want to rewrite mydomain to domain
you must somewhere specify what to do with domain