I think for a beginner, it's going to get complicated to do what you want - you'll need to ask the Finder to give you a list of all the Bookmarks in a particular folder, then reference them one by one.
I think a far simpler solution for you will be to keep a set of well named upload Bookmarks and then reference them directly, so you could simply have:
connect "UploadBookmark1"
using connection "UploadBookmark1" list local folder "/Users/username/Sites/myfiles"
using connection "UploadBookmark1" list remote folder "/public_html"
using connection "UploadBookmark1" upload "files"
using connection "UploadBookmark1" upload "includes"
using connection "UploadBookmark1" upload "graphics"
using connection "UploadBookmark1" upload "index.php"
disconnect "UploadBookmark1"
connect "UploadBookmark2"
using connection "UploadBookmark2" list local folder "/Users/username/Sites/myfiles"
using connection "UploadBookmark2" list remote folder "/public_html"
using connection "UploadBookmark2" upload "files"
using connection "UploadBookmark2" upload "includes"
using connection "UploadBookmark2" upload "graphics"
using connection "UploadBookmark2" upload "index.php"
disconnect "UploadBookmark2"
repeat as needed ... etc., etc.
Yummy will look through all your Bookmarks until it finds a matching name, so this will save you having to script the Finder to get information about folders and files.
For the Bookmarks, select 'Show All Bookmarks' from the Bookmarks menu which will show you all your Bookmarks. You can then use the facilities there to create / duplicate / edit / rename / delete Bookmarks.