Despite what some negative reviews have said, it actually is possible to have two characters overlap each other, it just takes a bit of figuring out: specifically, you have to use the barriers of the boxes to "cut off" the body part you want to appear over the other character, then use copy and paste and move the character to the exact other side of the box so that only the arm, leg, head whatever is visible, and line it up with the rest of the body. That's the real tricky part: lining up the figures so that (for example) an arm is where it should be requires so much precision that it's basically trial and error. Extremely difficult, but (theoretically) possible.
Having said that, I would highly recommend ONLY buying this program on SALE. I managed to get the program and three DLC for roughly 20 dollars total, and I still feel like I overpaid. But I suppose that's all the more reason to make the most of it.