Hi again. Yes you can blend together the images using different blend modes for their respective layers. What are the dimensions of the MDF you're carving? I'm pretty sure the Shapeoko will be able to handle it, size-wise, as long as you get the 32x33 version.
In PixelCNC I'd start by setting the canvas Z-Fill to the top of the project's canvas volume (click Canvas Properties on the left). From there you can load in your images as raster-layers and depending on whether they are black-on-white or white-on-black you might need to invert them (edit; toggle the invert option on the layer's properties) , and then use either the subtract or minimum blend modes, then scale and position them. The bottom-center layer handle moves the layer along the XY plane when left-click-dragging and it will move the layer vertically when right-click-dragging. For the top-center layer handle the left/right click are reversed. Left-click-drag it to scale the layer vertically.
You can email your PixelCNC project to [removed] and I'll take a look at it for you :)