I find it pretty hard to hand applique through a bonding material.
The way I was taught needleturn applique, you turn under the seam allowance as you hand sew -- no bonding material used.
Fusible applique is usually finished by machine because the machine has no problem getting through the bonding stuff.
Maybe I should add that my favorite applique method is machine applique with turned-under edges using the freezer paper method. I learned this technique from Harriet Hargrave's book:
http://www.amazon.com/Mastering-Mach.../dp/157120136X
She describes other machine applique methods in that book too, including fusible applique, but not needleturn applique because that is a hand method.