I'm trying to figure out what you did .... :(
You "sandwich" the handles between the lining and the outside fabric. Think of creating a sandwich with the wrong side of the lining up; Handles are placed underneath the lining and the raw edges of the handle are even with the raw edge of the lining; the last layer is the outside fabric positioned so that the right side is touching the handles.
I sew around the top before turning the bag right side out. Then you can do some stationary or top stitching around the edge around the top. This top stitching will also help stabilize the position of the handles.
Good luck :) :) :)