Are the trolls ecto-related? Like how the kids are? Does the process take into account the genetic reproduction of a species, and thats why they have the kids 'related'?

Karkat’s group isn’t related to one another. Technically speaking Meenah’s group would be, but the trolls don’t really have a concept of “related to one another” outside of ancestors and we don’t know how they’d be related. Either they’re just a mix of all 12 trolls, or 4 sets of 3 mixtures, or (and I personally find this one the funniest) that Karkat had to pair off his friends and assign them a <3 and <3< reproductive partners.