Start by cutting out both cookie pieces.
Use the same cutter or another cutter to remove the piece(s) you don't need.
Put the cookie pieces together on the baking sheet. Gently mush the edges together to "glue" the cookies into each other as they bake. Sometimes gluing the cookies together is enough, if they are interlocked and share enough edges. Sometimes though... you need to add some "tape."
It can be hard to see past all the lines and "Frankencookie stitches" to the design you have in your head. Don't be afraid to draw your icing lines on top of the baked cookie.
Please say example #2.
Because that would be the right answer.