What is the proper order to boot Macbook with Thunderbolt display?
The best guide to reference here is : http://manuals.info.apple.com/MANUALS/1000/MA1594/en_US/thunderbolt_display_getting_started.pdf

To use your Apple Thunderbolt Display with your MacBook Pro lid closed:


Connect an external USB keyboard and mouse to a USB port on your display, or use the
Bluetooth® Setup Assistant to set up a wireless keyboard and mouse.
Make sure your MacBook Pro is turned on.
Close the lid on your MacBook Pro to put it to sleep.
Wait a few seconds, and then press any key on your external keyboard or click the mouse to wake up your MacBook Pro