It sounds like you need to use a Walking Foot because of the multiple layers that you are now dealing with. That would help all the layers feed through together.
I believe the needle you are using is too large, designed at size 16 for very heavy thread. The needle being too large for the thread can cause puckering because the thread moves about too much when the stitches are being formed.
The needle size should to be selected to FIT the thread you've selected for the project, and secondly the task. Size 16 needle is very large. I don't have any C&C thread, so I'm not sure what it's weight is, but I bet it's not so much as to need a size 16 needle.
If I were to guess I would try a Quilting Needle (sharp tip) in size 75/11 or maybe a 90/14. Make sure you are threaded correctly, then put on a walking foot.
Hang in there!