Whatever marking tool you use, make sure that you test it on scraps of your fabric before marking! Also, I would not choose a quilting pattern that closely follows the piecing. No matter how carefully you secure the layers, there will be some shifting and precise quilting is going to be off on the back. I would do an edge to edge.
I use thumbtacks to align. Place the tacks thru the back in the places you want to align. Put a piece of painter's tape over the heads. Place the backing on your pinning surface & secure. CAREFULLY lay the batting on the backing without sticking yourself ;-). Now you can lay the top on, using the tacks to align. Again, be very careful. Pin securely, then remove the tacks.