Once you've made all the changes you wish, you can either zip it all back up and upload that one file to the Duet via the DWC, or you can replace individual files in the /www directory.
Hint: If there is both a "whatever.xyz.gz" and a "whatever.xyz" file in /www, the .gz will be used. So either .gzip everything, or put the SD card in a PC/Mac and totally clean out the /www directory before putting your stuff in.