They probably won't disappear. Sometimes you don't sweat the small stuff and to me, a few little wrinkles is small stuff on such a pretty wall hanging.
If you put anything puffy under your fabric and then embroider, you are probably going to get wrinkles. The only time I have used batting or fleece when embroidering was as a last step after the embroidery was done and I was going around a block, so I really haven't done what I think you did. I'm not sure of the proper methods and stabilization needed to puff the embroidery so that the center of it stands out.
This is a good little info article regarding stabilizing fabrics. There are many more out there on the internet.
http://www.embroiderthis.com/hofafor....7LS4s1O1.dpbs
This YouTube video shows how they puff baseball caps
https://www.youtube.com/watch?v=1Bzas8Ak4gM