Thanks for all of your help, both of you.

wmctrl -l | grep panel
0x01a00004 -1 xubi xfce4-panel
0x01a00034 -1 xubi xfce4-panel
0x042000cb  0 xubi [Solved] Keep panel at desktop level (Page 1) / Desktop / Xfce Forums - Mozilla Firefox

...it also returns any window that might have the word "panel" in it. To make sure we only get the xfce4-panel IDs, I would suggest something like:

ID=$(wmctrl -l | grep xfce4-panel$ | sed -n 3p | awk '{ print $1 }')

#!/bin/bash

# Wait for all panels to load
while [ "$(wmctrl -l | grep -c panel)" -lt "3" ];
do
   sleep 0.05s
done

# Determine identifier
ID=$(wmctrl -l | grep panel | sed -n 3p | awk '{ print $1 }')
# Place panel at desktop-level
wmctrl -i -r $ID -b add,below

Save the script and add it to startup programs (xfce4-session-settings). Please note that this script is focusing on hidding the third and last panel.

wmctrl -l
wmctrl -i -r 0x0120004d -b add,below

Then we need to make sure that windows will be able to maximize over the panel. This can be done with the following command from this thread:

xfconf-query -c xfce4-panel -p /panels/panel-2/disable-struts -t bool -n -s true

It works perfectly for me now.

wmctrl -l

...then

wmctrl -i -r 0x01600034 -b add,below

...makes the bottom panel not show up on top of windows. However, when I maximize the window, it still doesn't automatically cover the panel. Must be a setting for that somewhere.....

EDIT: Found it. disable-struts property. See here: http://forum.xfce.org/viewtopic.php?pid=24102#p24102

I don't want to send my panel to a specified desktop, I want to make it stay below all other windows as a dock.

But thank you for your answer anyway:-)

have a look on wmctrl.

"wmctrl -l" give you the list of open windows, and the desktop level (typicaly 0, 1, 2 ...). Xfce-panel for exemple has a -1 desktop level.
wmctrl -r <WIN> -t <DESK>   Move the window to the specified desktop. Maybee it works with -1.

(sorry for my poor english, i'm french)

I'm normally a fluxbox guy, but are supporting my parents' Xubuntu installation.

In fluxbox I have the option to but a certain window or panel at the desktop level, which is lovely, because your panels won't pop-over your windows all the time.

Is there any way to make a panel stay behind all windows all the time? So that you would have to minimize all windows to use it?