Hi Dan
I have not tested this but what you can do to accomplish this during the installation is to leave the application name field blank when installing with WebPi.
As far as moving the current site you could do either of the following ( again not tested)
a) Change path of the Root of the website to point to the location where this is currently installed ( i.e c:\inetpub\wwwroot\Acquia-drupal) . In IIS 6.0 this under site Properties > Home Directory > Local Path. In IIS 7.0 this is under Advanced Settings > Physical Path.
B) Assuming you are under a default path c:\Inetpub\wwwroot for your default website you could backup the current content in this folder then copy everything under c:\inetpub\wwwroot\acquia-drupal to this directory.
For the second question from an IIS perspective, I think you mean create another website with host header (http://anothersite.myserver.com) and point that to the current physical directory where Acquia is installed or a copy of the current installation files in another folder, but I am not sure if that achieves what you want.
I did some checking on the Drupal site and I did see a mention of multiple sites so it may only be available via their installer. You can contact Acquia-Drupal's support forums here and they should be able to answer this.
http://acquia.com/forum
Hth
Richard