I would like to re run say a toolpath in just the bottom left layer.
Here's the steps leading up to the end:
...Then just increase the freshly created raster-layer's "Background Z" to be at the top of the canvas, and invert the layer (both on the right-side of the window when a raster-layer is selected) which results in the original image I uploaded. Then create a new operation just like the original one but when you generate a cut-path it will leave everything else alone and only generate cuts within the area masked off the rest of the canvas. You're just changing the contents of the canvas so that generating a cutpath won't cover the entire thing anymore. You might need to set your minimum cut Z depth to something like 0.001 depending on the operation, so that it doesn't generate cutpaths across the top of the canvas (which it might if min cut depth is set to zero).
Create a paths-layer and then enable edit-paths mode.
EDIT: The UI is pretty much staying as-is, it's been under development for 3 years and while there are some things I wish I had in mind earlier during development the plan now is to finish the major features and get to beta sooner rather than later so we're going to go with a built-in help/tutorial/walkthrough mode that hilights what users must do in order to achieve different things. Have you looked at the included User Guide? It documents everything the UI exposes to users and explains a lot. It's updated for each released version.