I only use Steam a Seam 2 fusible & the paper comes off before you iron. I'm not understanding what paper would still be attached when you are ironing the applique piece in place.
I found these directions for the Wonder Under. Have you tried using their "alternative" method. That's more like how I use Steam A Seam2
How to Use Wonder Under Fusible Web:
Press and Cut - Place the rough side of Wonder Under against the wrong side of fabric. Press for 5-8 seconds with a hot, dry iron. Let cool, draw desired shape onto paper backing, then cut out.
Alternative method: Trace shape onto paper backing, cut to size, then press, rough side down, onto fabric. (note: avoid backward letters and numbers - draw on rough side of Wonder Under with a ballpoint pen. For dark fabrics, redraw shape on paper side.)
Peel and Fuse - Gently peel off paper backing. Position fusible fabric, web side down, on the project. Cover with a DAMP pressing cloth.
With iron on the wool setting, press FIRMLY for 10-15 seconds (heavier fabrics = more time). Repeat, lifting and overlapping iron until all fabric is fused.
Remove press cloth and iron fabric to eliminate excess moisture.