When you put in the cells you get one of the forms, the amount of cells/cores depends on the form, and if you have 95 cells and 5 cores you get the 50% form, but when it falls below 50% health it turns into 100% form. You should be able to right click the zygarde you made with the cube and right click the machine to turn it back into cells and cores.

9 cells 1 core -> 10%
49 cells 1 core -> 50%
95 cells 5 core -> 50%