Literally, you can poke the probe anywhere. Seeing as you went with the full config (switchable RGBS) then switch green into probe mode and then just prod your way around everything. If you've got a board that works that'd be even better for getting used to the tool as you'll know what should be displaying and you'll be able to see various parts of the graphics flying around the board busses.
This one really is just a "probe it and see" method though. Until you've got a faulty board with schems, it's not much use to highlight specific chips other than googling for "74 series multiplexers" or "74 series demultiplexers" as this is how graphics layers are often combined.
Just give it a bash and if you feel you've not learnt anything after an evening of trying, then we'll do some more targetted investigations. But with respect to MBWL, probe away. We don't have schems and we aren't sure it's got the right ROMs so I'd just use it as a sampler to see what you can find.
Recalling the video you shot, the outer "frame" which shows the score, any weapons/tools you've picked up and the number of lives left seemed to be rendered unscrambled, so you could probe around until you've found those.
But as I mentioned above, it's not just for chasing GFX through the board till you find where they get scrambled; there are all kinds of timing signals on the board and the video probe is an excellent way of viewing these in a way that makes more sense than on a 'scope. For example, on a Vulcan Venture I was working on, I managed to find the part of the circuit which muxes (multiplexes) in the various graphics layers. Just by walking down the pins of this chip you'd see the player space ship highlighted in green, moving down a leg shows me the score highlighted in green, another pin shows me the bullets, another the enemy characters. That's pretty useful to work back from the pins to chunks of the boards to see what part of the board is doing what.
So to summarise in one sentence "just probe away - it's the best way to learn"
