I am not sure what you mean when you say, "prewash only the quilt fabric". Do you mean only the fabric being used for the applique motif and not the background fabric?
Yes. You are correct.
For this invisible machine applique technique prewash only the quilt fabric for the applique shapes and motifs. This washing removes any dirt or crud from shipping or handling and shrinks the fabric.
Then, check all of your fabric choices for bleeding fabric, even your background fabric. Obviously, finding out a fabric is bleeding after you've used it is not fun.
Once your applique block is complete, you'll then wash out the glue. During this washing, your background fabric will shrink (if it's going to shrink). This shrinkage pulls your zig zag stitches to the back side of the applique, making them even more invisible.
Thanks for asking the question. If anything is not perfectly clear in my instructions, your questions help me get it right for future readers.