Dual monitor setup macbook 13'' pro retina
If I understand your configuration, you have:

a. macbook, plus two external displays

b. two thunderbolt ports, one for ethernet, one for display

c. one hdmi port for the other display

For the VGA display, you need a Mini DisplayPort-to-VGA adapter.

And the HDMI display can be simply hooked to the HDMI port.

Now, to display different desktops:


Go System Preferences >> Mission Control
Tick the Displays have separate Spaces
Set the other checkboxes according to how you prefer to work.
After step (2), you will be able to set different desktop backgrounds (for each display; the background will be reused when you add Spaces to a given display).