Hi,
briefly, if you create a blank site and select it to run on the specified domain, it will show blank page if no structure and layout is defined in CMSDesk.
You can always access the CMS Desk or CMS Site Manager using the urls:
<yourdomain>/CMSDesk
or
<yourdomain>/CMSSiteManager
From your description it seems you want to achieve scenario which is described here in Developer's Guide
Running multiple websites articleHope this helps to understand the principles we use.
Regards,
Zdenek C.