Cutter on top is by far the safest setup. You should not need to exert much downward pressure if your panel is properly flattened beforehand. The downward shear angle of the blades will exert the necessary downward force on the panel when the panel is underneath. Your job is to push forward and against the fence and of course with sufficient down pressure to keep control.
Reversing the rotation and flipping the cutter means you will be pushing the panel from left to right. If you are right handed, you may find this maneuver very uncomfortable.
Proper shielding, shrouding and TWO push blocks are essential. The rub collar is essential to reduce the span and the "black hole" between the two ends of the "fence". Your "fence" will probably be a 1/4" piece of plywood with a hole cutout to clear the shaft and the rub collar. Look for articles by Lonnie Byrd, his shaper advice is how I set up my operation. and as said by others, don't expect to take it all off in one pass.
The back cut operation will be separate and there you will cut with the cutter below the panel. You will use a different fence setup for this then as mentioned before.
If you someday plan to cut arched panels on the shaper, you will need heavy duty paneling sleds like Weavers or at least Woodhavens sleds. Don't try this until your are comfortable with straight cuts. Good luck.