normally your applique is all done before the quilting process- so when you don't want to stitch over the appliques you stop and start- if you don't mind your applique stitching to shop up on the back- as additional quilting over the cross hatch you could apply them after the cross-hatch--just remember the applique stitching will be on top of the cross=hatching on the back of the quilt-
it is up to you if this is a problem or not.