SiteAssist needs all files for the site to reside at the Ddreamweeaaver Site Root location.
the best way yo acomplish this is to create two separate local folders with 2 seperate Dreamweaver Site definitins.
Local Folder; C:\websites\mainSite
Local Folder; C:\websites\subSite
then have them put together on upload to the remote host:
host directory; httpdocs\
host directory; httpdocs\subSite