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.
