Sorry for taking a bit to reply. I'm currently backpacking in East Europe so been a bit busy.
In any case, I imagine you've been able to add the video files to the media pool in the Media view. After that and when you are in the editing view, after you have dragged your first clip in and there is a timeline with V1 and A1, just right click on the area above the V1 and select "Add track". That will add a second track you can put footage on and it will overlay the stuff on top.
Now, if the video isn't transparent (eg. browser window), switch to the Color view. First select the clip with the timer (the edit timeline shows up in the middle, you can scrub around). Then, there is the eyedropper tool (7th icon around the middle toolbar row). Select the eyedropper, then click on the color of the background in the top preview window. In the preview up top, above it is, another toolbar. There's the icon that looks like a magic wand. You can use that to toggle to see what is selected for guidance.
Now, at the bottom, right of the color bars, there is the "selection range". The last button there inverses the selection, so click that. Next, in the top right corner where the nodes are, right click and select "Add alpha output". Now, drag from the triangle in the bottom of the node in the center to the blue marked box on the right. That should do it.
You can use the bottom left sections "Qualifier" and Matte Finesse (blur radius might be useful) to adjust the selection if it wasn't perfect now that you can see the final result in the preview.