Hello,
There isn't any way to set the App Store to only update some apps. It's either all or none. Any that were purchased/installed outside of the App Store can be set to automatic or manual, depending on the app.
Any that aren't fully 64-bit won't be compatible as you know, and it's up to the vendor to make them compatible going forward. If they aren't 32-bit now, even if they are updated to another 32-bit version, they still won't run. So, since you have been checking which apps won't be compatible, don't install Catalina until all the apps you use/need are compatible.
macOS will prompt you when Catalina is available. Major macOS version upgrades aren't the same as updates, so Catalina will require you to approve the install. It won't install automatically, even if you have all of the checkboxes checked in the App Store preference pane.
Hope that helps,
C