There's an Adjust tool that enables you to resize any block in the layout, so you can have different size blocks in the same quilt. Click here to see an example. Each quilt can have three layers. Layer1 is your basic quilt design. Layer 2 is for appliqu overlay, and Layer 3 is for quilting stitches.
Layers work independently of each other.
What's really fun is you can see exactly how your quilting pattern is going to look on your quilt, and you can extend it into the borders as well. You can use the quilting stencils included, or you can turn any block into a stencil. You can also change the thread color of both layers. Take a look here if you want to see a screen shot of the quilting stencils in action. If the block can't be easily paper pieced, the preview will suggest dividing into individual segments and give you the piecing order within each segment.