The changes will be to your remote hosted database.
The bits that will need adjusting in yor PowerStore database are:
ID - - Name - - Value
1 - - Root URL - store/
9 - - Local Root - - /store/
10 - - Remote Root - - /store/
The reason that its best to define your store directory as the local root directory while you're working on it in Dreamweaver, is to ensure that the structure (and internal references based on that structure) of the PowerStore directory remain correct relatively.
Just as a small example, if you wanted to change the validation messages for any of the forms in PS3 or make new validations by using the WA Server behaviours, create a new database connection to use a different user, password or database for the store, or (for instance) add your own custom styles to the HTML Editor for the products or the CMS, then - without making Dreamweaver see the store as the root directory - it will create a whole new set of supporting directories outside of the store folder in what it has been told is the root folder instead of updating the existing ones in the store folder.