Dual monitor alignment on Ubuntu 12.04

Have you tried arandr? It's a GUI for xrandr and it's perfect to play around with multiple monitors/resolutions.

sudo aptitude install arandr

Hereafter you can see the interface. With the green tick button you can apply the current screen layout and you can also it to a file, which basically contains a xrandr command, to execute it whenever you want, for example at system startup.

you can easily set the desired position of the two screens with the --pos option of the suggested xrandr command.

In your case this would be something like:

xrandr --output LVDS1 --mode 1680x1050 --auto --output VGA1 --mode 1920x1080 --rotate right --pos 1680x0

For my quite similar setup this creates two hot corners in either of my two screens in gnome-shell. Don't know about fallback environment though.

Note that you have to adjust the "--output" identifier according to the ones returned by the command xrandr | grep connected.

xrandr --output $1 --mode 1680x1050 --primary --auto --pos 0x240 --output $2 --mode 1920x1080 --rotate right --pos 1680x0

This should be the proper command. Think of your desktop as huge unified picture with dimension 2730x1920. The primary display (defined by --primary and doesn't have to be the first display configuration in the options) is positioned 240 pixels below the top to align with the 2nd monitor at the bottom. Instead of --pos 1680x0 the second monitor could also be aligned with the --right-of option. Of course you need to replace $1 and $2 with the proper names of the connections as Nix mentioned.

With this setup Conky should display properly when configured to align to the lower left as this space is now visible. When it's aligned the top left, you would need to add 240 pixels of spacing in this example. The part with the desktop shortcuts sound like a bug. I recommend not using many desktop shortcuts or not using them at all. :)

You could also leave the --mode options out since --auto already does that.