The eCart files will all be stored at the rot of the Dreamweaver site.
using your currant setup, you need to create a uniquely named eCart object for each subsite.
another way to go about it is to create new Dreamweaver site for each sub site, and "put them together" when uploading to the server.
Site folder: c:\websites\site1
Site folder: c:\websites\site2
Site folder: c:\websites\site3
them on the remote tab, set then upload to:
host directory: httpdocs/site1
host directory: httpdocs/site2
host directory: httpdocs/site3