Domain Mapping on WP Multisite

I have the Domain Mapping plug-in installed but the option to map domains doesn't appear on the primary site. Is domain mapping only possible on subdomains and reside under a primary?

Here's some more detail.

I was building out our site under and transitioning from the old flash site that resided on The site is now done, and I pointed the dns for to the WP IP address.

It works, but the user is first greeted with a URL, but the links on the site all then change to (what the site was originally built under)

I would like to change that so all links go back to

I also need the ability to create landing pages that have different branding and appear under different domains (for example, and and those mini-sites reside in the same WP installation so that I can share images/etc but have different branding on each.

Is this possible with WP MU and your plugins?