Play around with it and see what looks/feels best to you. I treat this problem differently depending on the collection. When it comes to Disney characters (for me, this would be Snow White, Belle, and... otters), I prefer to group certain pins by sets rather than break them up by characters. This applies more to stylized sets like vinylmations, sorcerer hats, etc. When it comes to park pins, however, I only arrange them by lands and attractions, because that makes the most sense to me. So if I had a topiary set from EPCOT (or wherever, I'm not super familiar with those), I'd want to break it up by Future World/World Showcase countries, rather than keep the set together.
I have no idea if that made sense or if it's helpful. Good luck, though!