The additions of groups to the new map viewer is very helpful and makes organizing maps with many layers very easy. Unfortunately, if you plan to use that map in a story map and individually display some of those layers, then you can't use groups as the story map will only give you the option to show and hide all grouped items rather than the layers nested under it. This is what the layer looks like in the ToC of the web map:
In the Story Map, you only have the option to toggle off the group. You can't show or hide layers indivdually.