To answer your side question first, I think you can use inkscape to convert the objects in the pdf to paths before exporting as an svg, and you won’t have to go through sketchup.
You can import several sketches into one estlcam project. I’m not sure if the auto selection will treat different sketches differently. I also don’t know if the different layers will line up well once you import the different pieces.
In case you aren’t aware, there is also a sort of in between mode, when you are doing manual, but using the right click instead, to let it follow curves and things:
As another alternative, you could create different gcode files for each “layer” and then combine them all together before you did your job. That’s not ideal though.