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Most certainly mark it before you sandwhich the layers. There are a lot of premarked wholecloth items available. I have done one queen size quilt and at least a dozen smaller items. It is a joy to quilt them because there are no seams to contend with and it goes fast. At least for me. I like to use colored thread for my quilting. It reminds me to do a good job as the stitching will certainly stand out.
There are lots of marking tools out there. Be sure to read the directions. If you plan on doing crosshatching I recommend not marking that. Just use lengths of either masking tape or the new blue masking tape. That way you just stitch along next to the tape and move it to make the next set of lines.
Remember that your spit will take out your blood. A white on white will definately show blood stains.
Be sure to show us a picture of your finished product.