When you are checking on or editing the SecurityAssist rules it checks for the WA_SecurityAssist folder in the root of the site. If it is not in the root of the site then the rules will not be available to you for changing.
It is similar for the templates, any template file must be within the site root in the Templates folder. If the template is not in here it will not be found by DW.
One way you can do this is to create a new site in DW and set the folder for the site to be the folder you have all of the PowerCMS stuff in. This way the rules and templates will be available in the root of this new site.