Content Docker Help

I can't figure out why my folder in the content docker doesn't follow the normal folder tree. I have a folder that I keep open on every new page. This folder also has a folder in it with other bits I use but only once in a while. There is a lot of stuff in that folder. The parent and child folders show up in the docker as if they were combined.
I.e. the parent folder has patternmaking details which contains a lot of things like notches, pattern directions, grainlines which are used on a pattern and the child fp;der has things like buttons, buckles, ruffles and bows which are things that are not used all the time, yet this shows up as one large file with everything mixed together.
Also when I tried to include another folder of the completed patterns it came up with everything including images of the samples. Each pattern is in it own folder and in that is an images folder and the total folders in this file are near 2k so having all these photos open as well as all the folders open Parent>child>grandchild all mixed up it is just crazy. I think I must be doing something wrong.
Thanks for your help