yes, you will have to upload from both Dreamweaver Sites.
For the existing site, set the Host directory on the Remote Info tab of the site definition to:
public_html/
For the power store site, set it to:
public_html/store/
this will put the site back together when it is uploaded to the server.
The error message you are getting is saying that there is not a localhost connection created to connect to the power store database. Once you have the power store files in place and edit the Connections/localhost.php file to connect to the powerstore database, you will fix that error.
I THINK I did everything you said to do. I checked and rechecked my settings in site manager against your instructions. I went to the site you linked, updated my IIS to 7 (I had six, so the instructions weren't working), set up a virtual directory...not 100% sure I did that right, but I don't have a way to know except to try the connection in Dreamweaver.
Went back into Dreamweaver and went into Databases, clicked the +, chose MySQL Connection.
Assigned the Connection name as powerstore
MySQL server: localhost
User name: admin
Password: root (I tried not using a user name or password since I never assigned one anywhere on the local virtual directory. If the virtual directory has a "user name" I never set it..and would have no clue how to find it, so I used the user name and password in the WA tutorial on setting my the MySQL Connection thinking maybe it is a default??)
Database: [clicked on the "Select" tab] I immediately get an HTTP Error Code 500 Internal Server Error
Man, I wish I could just get this thing to work!