Here is some good advice about making the cookies that I found on the Her Interactive forum:
First, look at the middle section to see what is there and put that on the bottom cookie. The hardest part about this is seeing if there is a jam or if it is just a plain cookie with sprinkles and/or frosting.
Second, put a top layer on the cookie (from the upper left corner).
Third, compare the cut-outs with the rest of the top of the cookie. If the toppings are only on the cookie and not over the cut-out, put on those toppings and then use the cut-out. If the toppings are over both the top cookie and the cut-out, then use the cut-out first and then put on the topping.
The key is making sure the toppings are layered correctly.
Let us know if this helps.
