Place media on track two
Place logo on track one
The only thing you will see at this point is the logo
Use either event pan and crop or track motion to resize the logo to the size and placement that you want it.
Click on event Fx on logo event and choose chromokey. Use dropper to choose the black background on the logo.
You should now see logo (with no back background) superimposed over the media on track two.
Vegas sees from the top down. You will see whatever is on the top track unless you resize it or change the opacity to see what is beneath it on track two and so on.