Try a sample using your invisible thread using the knot function and bring a sample of you bringing the threads it the back and knot. Check which you like best and check to see which method makes a more secure knot. After stitching all those pieces, you don't want the thread to start unraveling.
P.S. After hand knotting on the back, I run the thread tails under the stitching in the back about an inch and then trim the thread end. It keeps the back neat and prevents any knots from unraveling.