What kind of commands can I add to Advanced Setup?

You use the same commands you would use in a terminal to start the application. As a matter of fact it is a good idea to Start and Close the application you are planning to add in a terminal. That will allow you to check if there are any error messages. Some errors can cause the application to "hang", making it appear Magick Rotation has stopped responding or won't rotate the screen.

Here are some Advanced Setup command examples (note use of semi-colon to separate commands).

[Run before switch to tablet:]
killall -9 cairo-dock; gconftool-2 --set /apps/panel/toplevels/top_panel_screen0/size --type integer 42

[Run after switch to tablet:]
cellwriter --show-window; cairo-dock -o

[Run before switch to normal:]
killall -9 cairo-dock; gconftool-2 --set /apps/panel/toplevels/top_panel_screen0/size --type integer 24

[Run after switch to normal:]
cellwriter --hide-window; cairo-dock -o

CellWriter is included by default; the commands show it in portrait and hide it in landscape. The Cairo (or Glx) Dock commands are to close the dock and restart it after rotation so it resizes correctly. The gconftool command resizes the top panel to a larger size (from the default 24) in portrait so it is more touch friendly.

Depending on the model of tablet PC you have you might experience, while in tablet mode, inadvertant key presses and/or touchpad or trackpoint (Thinkpads) input. Those can be turned off through Advanced Setup also. Determine the "device name" for the offending input device with 'xinput list'. Then enter the needed commands as demonstrated in the following examples:

[Run before switch to tablet:]
xinput set-prop "AT Translated Set 2 keyboard" "Device Enabled" 0
xinput set-prop "SynPS/2 Synaptics TouchPad" "Device Enabled" 0
xinput set-prop "TPPS/2 IBM TrackPoint" "Device Enabled" 0

[Run after switch to normal:]
xinput set-prop "AT Translated Set 2 keyboard" "Device Enabled" 1
xinput set-prop "SynPS/2 Synaptics TouchPad" "Device Enabled" 1
xinput set-prop "TPPS/2 IBM TrackPoint" "Device Enabled" 1

0 is off and 1 is on.