I sew it through all the layers... I have only put aplix on vb aios and the soaker pad is supposed to fall below where the loop aplix is sewn on, so really I'm only sewing through two body layers and the pul. Once I made the mistake of making the soaker pad too long and tried to sew the aplix on it and it threw my machine all out of whack!! I had to take it in just to get the tension fixed!