Why not setup multiple instances of dropbox? I have 2 dropbox accounts which I've setup like so:
$ ls -l ~/Dropbox
drwxrwxr-x 10 saml saml 4096 Nov 30 22:21 personal
drwxrwxr-x 10 saml saml 4096 Dec  7 15:49 work
Inside each of those directories is a Dropbox folder:
$ ls -l personal/ work/
personal/:
drwxrwxr-x 10 saml saml 4096 Nov 30 22:21 .
drwxrwxr-x  4 saml saml 4096 Dec 14 20:49 ..
drwx------  3 saml saml 4096 Nov 30 22:20 .cache
drwxrwxr-x 19 saml saml 4096 Mar 19 11:30 .ccache
drwx------  4 saml saml 4096 Nov 30 22:23 .config
drwx------  3 saml saml 4096 May 15 11:00 .dropbox
drwx------ 17 saml saml 4096 May  8 22:13 Dropbox
drwx------  3 saml saml 4096 Nov 30 22:21 .kde
drwxrwxr-x  3 saml saml 4096 Nov 30 22:20 .local
drwx------  3 saml saml 4096 Nov 30 22:20 .pki
work/:
drwxrwxr-x 10 saml saml 4096 Dec  7 15:49 .
drwxrwxr-x  4 saml saml 4096 Dec 14 20:49 ..
drwx------  3 saml saml 4096 Dec  7 15:49 .cache
drwxrwxr-x 18 saml saml 4096 Feb  5 10:03 .ccache
drwx------  4 saml saml 4096 Dec  8 22:18 .config
drwx------  3 saml saml 4096 May  8 22:13 .dropbox
drwx------  5 saml saml 4096 May  8 22:13 Dropbox
drwx------  3 saml saml 4096 Dec  7 15:49 .kde
drwxrwxr-x  3 saml saml 4096 Dec  7 15:49 .local
drwx------  3 saml saml 4096 Dec  7 15:49 .pki
My content is inside the Dropbox folders for the 2 accounts. I then use this script to start up my dropbox applets.
#!/bin/bash
dropboxes="personal work"
for dropbox in $dropboxes
do
    HOME="/home/$USER"
    DROPHOME="$HOME/Dropbox"
    if ! [ -d "$DROPHOME/$dropbox" ]
    then
        mkdir "$DROPHOME/$dropbox" 2> /dev/null
        ln -s "$HOME/.Xauthority" "$DROPHOME/$dropbox/" 2> /dev/null
    fi
    HOME="$DROPHOME/$dropbox"
    /home/$USER/.dropbox-dist/dropboxd 2> /dev/null &
done
This script is launched from the GNOME Startup Applications tool. The script is called dropbox.sh.
      
I setup the Startup Application so that it runs this command:
bash -c "sleep 60 && dropbox.sh"
This gives the network a minute to come up before starting Dropbox.
It's a little weird at first but you get used to seeing 2 dropbox icons in your taskbar.
                               