Make the source your system root `SOURCE="/"` and then create an exclude file at:
~/conf/
At this article there is a good example of exclude file: <
**/*[Cc]ache*
**/*[Hh]istory*
**/*[Ss]ocket*
**/*[Tt]humb*
**/*[Tt]rash*
**/*[Bb]ackup
**/*.[Bb]ak
**/*[Dd]ump
**/*.[Ll]ock
**/*.log
**/*.part
**/*.[Tt]mp
**/*.[Tt]emp
**/*.swp
**/*~
**/.adobe
**/.cache
**/.dbus
**/.fonts
**/.gnupg/random_seed
**/.gvfs
**/.kvm
**/.local/share/icons
**/.macromedia
**/.obex
**/.rpmdb
**/.thumbnails
**/.VirtualBox
**/.wine
**/Downloads
Also, you should not backup /dev, /proc and other system folders in a Unix system. Just add them to the exclude file.
If you mean multiple remote directories, you must create a profile for each machine:
duply server1 backup
duply server2 backup