You would make an image with all the squares you want attached. You can use the free getpaint.net, free inkscape or silhouette studio or procreate for iPad. It should be pretty easy to do in inkscape or getpaint.net - just make sure all the walls are the same thickness.
In Cookiecad choose imprint cutter and set imprint depth to 0. You’ll probably need to do a little trial and error with the experimental settings → thicken interior to get the inner lines the right thickness so they cut nicely. Here is a discussion about that.