Screencasting & Slider Master issue

I need to create a curriculum on new computer programs and the “record screen” function is absolutely fantastic. I've just recorded a 15-minute sequence which generated 60 slides. I recorded in 16:9 with a resolution of 1600x900 with the idea of enlarging to 1920x1080 afterwards, which leaves me with a 180 pixel footer to add navigation via the slide master. I consulted the forums and unfortunately I didn't see a solution to get around the screencast layer, which is always on top. Do you have a solution to suggest?