B and C are at the same position, maybe that is at the origin of your problem. To get a structure that reflects the fractional occupancies, you should add ONE atom at this site. Afterwards, you can modify the chemical composition as follows:
1) Select the atom
2) In the "Property Explorer" (usually bottom left corner), you select "Composition"
3) In the window that opens up, you first reduce the fraction of element B to the desired percentage, e.g. 60%, using "Edit". Then, you use "Add" to add element C and specify a percentage of 40%.
Your system seems to be a perovskite. If you use the highest possible cubic symmetry, the oxygen atoms are equivalent. You can specify the symmetry in advance in Materials Studio. Then, you need to add only one oxygen atom, and all others are generated automatically.