I also have 3 types of speakers and a sub. In this case, there are 8 small speakers, 4 middle sized, and 4 large.
The bass on the small speakers only supports a lightweight 8' stop and above. The middle size supports a light 16' or above, with the sub. The large supports heavier 32 and 16' stops and above.
Your speaker frequency ranges seem somewhat similar (not sure about the Mission model), where the 1030s are small, the 1031s are middle, and the Missions are large.
So I use 3 audio groups, "upper" for the small speakers, "middle" for the middle ones, and "lower" for the floor-standing speakers. The sub gets the middle and lower signal with a compromise low-pass filter to support both.
I assign ranks based somewhat on pitch and weight of the stop. 8', 4', and upperwork is split mostly between the upper and middle groups, with some on the lower group to balance out the sound. Heavier 8' stops are on the middle group for better bass definition. 16' stops are split between the middle and lower groups, and 32' are only on the lower group.
As to speaker placement, my upper and lower groups are both split equally between rear and front, and my middle group is front only just because of shelving space on the walls. I like being surrounded by the sound, so that works for me. For a surround set, I mix rear ranks freely in with front ranks and don't worry about location. Not everybody's preference...
That's just how I do it. There are other schemes, like putting each division on a single audio group, that work for people.