I spray basted a less than twin size recently and had lots of wrinkles on both the back and front. I took it to the person who demonstrated spray basting and asked him what to do about it. He said to press with hot iron. That would soften up the spray and enable me to smooth it out. I did this and it seems to work. I havn't started quilting yet but will iron again before I do. Also will pin with straight pins around the area I am qulting. Each square gets a motif. I was going to quilt in the ditch but pressed seams open and didn't have any ditches to quilt in so have to do a bit more elaborate quilting.
So, try ironing and smooth. ALSO, as you are quilting be aware of the back and smooth as much as possible.