If you install PowerCMS Builder to another site in order to have it in a sub directory of the main site, you wont be able to use the menu Dreamweaver menu access point to add new content areas, you would need to manually add the developer notes code to your apge in the other DW site.
I will put through a feature request to have it considered for the future to make Power CMS install to it's own directory, but for now, the only way to make this work is to manually create the content areas and copy the developer notes code.
as for the Serial number, It must be entered any time you install power CMS on a new server, this is not so much to keep track of the domains you are using it on, but to make sure you have a proper serial number to be able to install it.