Groups have only one purpose: to create those two related Hubs at the end of each Hub. That's all. The grouping on your profile page is determined by HubPages' categories, not your Groups.
So, the important thing is not having sub-groups, it's ensuring that for each Hub, the two Hubs either side of it (in the group) are the most appropriate - because those are the ones that will appear at the end of it.
You can re-order the Hubs in a group by dragging and dropping.