I understand your question (I think!).
First off, lay a large flat sheet down first to catch overspray. You can toss the sheet in the laundry afterwards and the spray will wash right off. It also helps to spray from the edge towards the center, to minimize overspray.
I usually don't tape down the backing fabric. It's enough for it to be flat and smoothed out. Smooth the batting out, then fold the top half of the batting down, spray and smooth back together. Do the same with the bottom half.
At this point, if you haven't taped the backing down, you can remove the batting/backing combo and lay the top down, smooth it out, and then lay the batting/backing combo on top. You can repeat the entire process, lifting the batting/backing combo back the way you folded back just the batting before.
Alternatively, you can just smooth the top over the batting, fold back the top halfway, spray, and smooth the top back.
The short answer to your question is that yes, you do need to spray both the batting and the back together and the batting and the top together.