MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
That's great you've made so much progress. The indents in the bottom are used to help keep rubber bands in place, assuming you use them to hold the stack of trays & cards together. You can sort of see that in use from some of the pictures.
They are definitely optional; I've considered removing them before. They generally worked better on the original Catan design any ways.