Okay, here's how it's looking for my prequel. You can link prequels to the series as "related". If you do that, and you do the series by numbering, the prequel will show the series, but will be without a number. Then on the series page it will list "prequel". Interestingly, when someone bought the series today, they bought my prequel. They hadn't been doing that much before, so it appears this is worth doing.
Linking the boxed sets wouldn't work well for me. My series name is "The Hawthorne University Witch Series". The boxed set is titled "The Hawthorne University Witch Series". So it would read "The Hawthorne University Witch Series (The Hawthorne University Witch Series)". This would be silly. So if any of you link your boxed set as "related", title it something completely different than the series.
Another thing I had to do was change the name for the boxed set. It used to read "Complete". Well, my boxed set isn't complete now because it doesn't include the prequel. Nor does it include my novelette prequel. I was able to delete the word for the ebook, not the print book. It turns out that on Amazon, you can't change a print book title--at least that's what customer support told me. Hopefully, readers who but the print book won't mind because they are purchasing a large omnibus. I don't know what else I can do (and it's already a huge paperback as is with 3 novels).