Is there an easy way to have a skatter group avoid another skatter group on the same surface so that I don't get merging objects?
That is not possible for now.Collisions only work within the same Skatter setup.
What you can do is generate your first setup in the model (no Render Only), then use this group as an Object Area in the second setup.
Thanks. How would I go about that?
More info: http://skatter.helpscoutdocs.com/article/68-areas#object_areas
Beware though as collision detection tends to be slower when processing with complex objects.