Each question bank activity will still have categories. If all your qusetions in one big question bank with carefully organised categories is what is best for you, then you can do that.
If, before the upgrade, you have questions shared outside courses (at system context and in course categories), then for those, the upgrade will make a new course to hold them, and create one question bank acitvity in that new course. The upgrade process will never create more than one question bank in any course, and it will only do that if it is needed.
And, once the upgrade has finisihed, if you want to change what it has done, you could then move the questions around, if you want them organised in a different way.
If, before the upgrade, you have questions shared outside courses (at system context and in course categories), then for those, the upgrade will make a new course to hold them, and create one question bank acitvity in that new course. The upgrade process will never create more than one question bank in any course, and it will only do that if it is needed.
And, once the upgrade has finisihed, if you want to change what it has done, you could then move the questions around, if you want them organised in a different way.