I'm not sure if this is intended functionality or not, so I could be wrong.
2 Different Domain names
Site A has the domain for Site B parked on top of it.
Here is what happens:
I type in http://SiteB.com into my browser. I get forwarded to SiteB.SiteA.com.
My understanding was that they would act as if they were independent sites. For example, I though it was such that you'd never know that SiteB was a subdomain of SiteA, and would always show SiteB.com along with any permalinks in the browser.