404 Error When Domain Mapping

I am having an issue with domain mapping. I get an 404 error after entering the domain in the Tools -> Domains in subsites. I also have the multi-domain plugin installed, and changed the sunrise.php to account for that. The multi-site is currently installed in a subdirectory, and it appears that the domain mapping makes the URL http://www.clientdomain.com/sites/ instead of just http://www.clientdomain.com. If you type the latter in the address bar after setting up a site, the site shows up but the formatting is all messed up. Thanks ahead of time.