The saddle shouldn't be anywhere near the horse's shoulders. If it is, you're placing it too far forward. The tree points should be 2-3" behind the back edge of the horse's shoulder blades. You can find the tree points by looking under the flap toward the top of the saddle, in front of the billets. You should see a little leather "pocket" with a hard lump under it. Those are the tree points.
Picture of the saddle would help. Put it on without any pad, lightly girthed up. Tie the horse on level ground, or have someone hold her. Make sure her head is in a neutral position (not on the ground or up in the air). Take a side shot showing the whole horse. Move toward the front of the horse and take a 3/4 front angle showing the whole shoulder, so we can see how the saddle lays against the horse. Take one more picture from the rear, stand on a stool if you need to. We need to see how the saddle sits against the horse's back.
With these pictures, we can give you an idea of what's wrong with the fit, if anything. An in-person saddle fitting is best though, if you have access to a saddle fitter in your area.