I always keep my small MEC powder bottle at least 1/2 full and never fill the large shot bottle more than 1/2 full. No science behind this, I just like them this way.
When I load for games using 5, 6, or 7 size shot, I only fill the shot bottle about 1/8 full. With larger shot, I sometimes get the shot clumped together in the bushing and the shot will not completely drop. I don't load many of these shells so it is not a big problem. I do a firm downstroke and immediately check to see that all the shot dropped.
I think the small bottle is just right for target loads. I like to load in lots of 100. So the small bottle is just enough for 100 1 1/8 oz loads. Comes out about 2 cups of shot and about 1 cup of powder.