The solution that Neilo proposes is one way to go about it, though Dreamweaver will throw an alert saying the site is contained in another site.
another way to go about it is to separate the sites locally, then put them back together when uploaded to the host.
What I mean by this is to have two separate site in Dreamweaver that each have a different local folder:
On the remote tab of Dreamweaver, set the main site to upload to www folder. and set the store site to upload to the www/store folder.
The error you are reporting is occurring because the power store files are not at the root of the Dreamweaver site.
OK - Great. What do I do now? I need to set up a store where the Power Store files are not at the root. This is because this particular store will be accessible via a password only. (Meaning you will not be able to even SEE the store without first logging in.)
This does go back to my frustration about lack of documentation. That is a huge thing that should be mentioned in some sort of FAQ about PowerStore. THat the files must be in the root of your site.
Is there no work around here? Could just the eCart and Template files be in the root - and could the index.php and other files be stored within a subfolder?