I haven't done this, but I would lightly spray between the two battings to make sure they don't shift away from each other. Cotton likes to grab cotton, so I would keep the spray really light.
It shouldn't make it more difficult to sandwich; you just have to make sure you use a good technique -- the standard one, where you position first, then peel back the top half, spray only the top half, smooth the peeled back portion back, then peel back the bottom half and do the same. If you try to spray the entire batting and then position the other batting on top, I can guarantee a huge mess!
The brand of basting spray you use might make a difference. After trying several brands, I use only 505 now. Have heard that the new Therm-o-Web is also very good.