Yes, your sewn top will have "stretch" because of the seams but PaperPrincess is correct. You have to sandwich your three layers together before you can quilt, whether by hand or by machine. Basting them, pinning them, spraying them - which ever you chose - will stabilze all the layers and then you will have successful quilting.
I am not on my computer now but if you use You Tube you can search for videos that show you how to do this. Search on "sandwiching a quilt" or "quilt sandwich". There are ways to do the sandwich a bit at a time when you don't have room to lay it all out.