The easiest way to do this would be using layers in an editor and selecting a colour to be transparent in the upper layer.
For example if you use debugmode wax (This is freeware), create an image with your logo. For example make a border rectangle in red and set all the other area to pure green rgb(0,255,0). Place the video on a lower layer and the image above the video. Now add a chroma key plugin and set a specific colour in the top logo image to transparent, in this case the green. The video shows through the areas that have been designated the chroma key colour.
For more info, go to youtube and look for "wax chroma key". There are many tutorials, most are for people in front of video background, but just replace the person with a still logo image. This way you can get what you want easily without the trouble of editing each frame individually.
Free Animation Software at www.HeliumFrog.com