Nick, in Fusion360, you can create a model, then use 2D toolpaths on that model by picking chains.

The only real benefit over using just a 2D drawing, is it allows you to see how the toolpaths are in relation to the model, which is handy for highlighting any issues (usually operator caused!). Regardless of 2D/3D toolpaths, you still have to ensure heights are correct for each toolpath, and you've set the part zero at the correct place.

Industry standard is you set Z zero on the surface and work downwards, but in Fusion you can set part Z zero wherever you want and adjust heights accordingly. If you're unsure about the heights, you should be able to go to a side view, and when altering any of the depths, they should be shown on the model.
Not all the settings may make sense if you're unfamiliar with the settings though, as there are options to alter where the heights are relative to.