No layers should be stretched--I did that when I first started and got lots of shifting/puckers when I pin basted. Then I shifted to spray adhesive basting and get
Much better results! It seems counterintuitive, but making the layers too Tight works against you as the layers are at different tensions and go through the machine at different rates. Just be sure all three layers are smooth and flat not tight.
Also be sure to use a walking foot so that both the top and bottom layers are feeding through your machine at the same rate. If you don't have a walking foot and are just using a regular pressure foot, you will likely need to reduce the pressure foot tension some to prevent a drag on the top layer.