The problem you decribe is what keeps many from using the satin stitch. Chances are that nothing is going to smooth it out now, how much did you do and can you pick it out?
With a satin stitch you need to loosen your tension slightly. Still need to use sablizer even if you use heat and bond because the outside edge of the stitch is hitting plain unbacked fabric hense the ripple. I like heat and bond LITE or steam a seam for most fused projects. always test on scraps.