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Jack Wolcott’s method of switching back and forth would be best, though I would not normally suggest putting a camera on anything being projected. You can get an Atomos Ninja 2, it will record any video signal (HDMI) that you put through it and will pump the signal back out for the screens. Then in post production you can AB edit the footage or play with the scale and position of the videos (or even crop the videos to the core subject) and place them side by side, though there will be inconsistencies if you are not using uniform scaling.
If you are low on time however, just make a note of what slide is used and when (according to your cameras timecode), then get the presentation afterwards. All you would have to do then is take the slides, screenshot or Snip them to make photos, and edit them in post production.
As for editing software I would suggest Adobe’s Premiere Pro. They do offer trial versions, which while they do not compare to the full versions, it will get you through this video.