Sure, you can use layers, but this is not a good or effective way to group instances.
I still don't understand you game. If those complex shapes are made from several different objects (Circle and Line sprites), then you can do this:
Add Circle and Line to a family "ShapeElements". Define an instance variable "ShapeID" on the family.
For all the circles and lines of the first shape, set ShapeID=1
For all the circles and lines of the second shape, set ShapeID=2
Now all 14 elements of your shape 1 are logically linked together, you can do "Circle compare variable ShapeID=1" and this will pick 7 circles.
Or you can "ShapeElements compare variable ShapeID=1", this will pick all 14 circles and lines.
(Family in this example is optional, but I assume that circles and lines share some features and properties, so adding them to a family seems like a good idea)
Linking by "parent.UID" is a bit different. You don't need to keep track of all UIDs, it's easier to give an example:
https://www.dropbox.com/s/kr2gy6xwi3gxq ... .capx?dl=0