First, your post points to a definite need for improvement in the way categories are listed on the options screen. If you have a lot of categories — it’s just a crazy mess to list them all right there at once. A solution is on the list.
Most importantly, though, I think you might misunderstand the purpose of the categories on the options page. If you just want to change content from published to draft, you don’t need to mess with the Category section of the options at all.
The Category section is so you can make changes to the Categories a Post is listed in when that Post expires. Here’s the gist:
1. You select some categories on the options page.
2. Above that, you tell Content Scheduler what you want to happen to a Post’s Category list upon expiration:
a. Set the category list to match EXACTLY the ones you’ve selected.
b. Add the selected categories to the post’s category list.
c. Remove the selected categories from the post’s category list.
d. Apply no change.
So, in your case, you probably just want to select “No change” in CS options under “Apply Category Changes As…”
Check out the PDF documentation that’s with the plugin. And, if you think it’s unclear and should be reworded, I’d love to hear about it — always trying to improve.
Paul