they run into this problem over and over and over again
You see it happening over and over again. Each of them is going through it for the first time. Teachers have to keep this in mind.
@LJRo, the Mordax Data is a good learning and debugging tool, but your case is too small for it. Even with it removed, your system is going to be limited and probably frustrating. If you stick with this case, you will at a minimum have to get rid of one of the larger modules. The better option is to think about a bigger case, and do some planning, with proper choices for envelopes or function generators, VCAs, and utility modules. You don't have to get it all at once; you can grow into it, if you choose judiciously.