since the PowerCMS Builder files can only be installed to the root of the Dreamweaver site, this is all controlled by how you define the Dreamweaver site.
you can set the Dreamweaver site to upload to a sub directory of your remote site by setting the host directory to point to the sub directory in the Remote Settings of the site definition.
The PowerCMS Files will be added to the Root of the Local Dreamweaver Site Files. where those files are uploaded to the remote server depends on how you configure the remote settings in your Site Definition.