This is a big terrain piece with many parts. Many of the parts may look similar, but each part is different. There is only one correct way this piece goes together. If something looks misaligned, then you are trying to put the wrong parts together.
I recommend you put the church completely together without gluing anything first to ensure you see how each piece fits together.
When gluing, I usually use clear Gorilla glue and use masking tape on the bottom of the pieces to keep them together until the glue dries.
