Richard, based on the test I made, you can upload the pages using teh Dreamweaver FTP (both in web and non web space, depending on what allows your FTP setup), but if you upload the DW pages in a non web space (such as the moodledata folder where course files are generally stored) , all external references (css, javascript, images etc.) will be broken. In this case it is better to zip your Dreamweaver site, upload the zip file from within Moodle, uncompress the zip then link to the file as resources: in this way all external references will work while remaining protected.
If you still does not like this way, you can upload your DW files in a web space folder after having protetcted them: i posted some info about this here.