Deja Dup is asking you where you want to store the backup files. It packages them up instead of storing them bare in the filesystem like using the
copy command would, so storing them on remote machines or in different locales isn't a problem.
By default I believe Deja Dup only backs up your home directory. An easy way to 'backup' the package-manager-installed packages, you can do
dpkg --get-selections > ~/Desktop/installed_packages.txt, and on the new system you can restore it by doing
dpkg --set-selections < ~/Desktop/installed_packages.txt and then
sudo dselect and going to
Install. That will download and install all the packages the package manager had installed on your old system, and by having the installed_packages.txt file on your desktop it will get backed up with the rest of your home directory.
I'm not aware of a way of forcing it to do a full backup, though it may be possible if you read through the documentation for Deja Dup and Duplicity (the program Deja Dup is based on).
Webdav = http://en.wikipedia.org/wiki/WebDAV