I also worked on ships, and have traveled on many as a passenger as well. I am sorry but I have to respectfully disagree with your assessment that higher is better.
BTW: I also did a Miami to NY cruise in December once on the HAL Statendam. We hit very rough weather.
First we need definitions: pitching & rolling. Pitching is the up & down motion that happens when a ship is perpendicular to the waves, sailing into them. This is the preferred way to sail into rough weather.
Rolling is the side to side motion you get when sailing parallel to the swells. This cause the ship to rock from side to side. This is less-prefered way to sail, but sometimes it is necessary.
Ship stabilizers can only reduce rolling, not pitching, because they are "wings" that come out from the hull and reduce the roll of the ship.
You were experiencing pitching, the feeling of the floor dropping out from under you. You felt better after you moved because you went more mid-ships, not because you went higher. The front of the ship is the worst place for motion because of pitching. Mid-ships is where you feel the least pitching. You feel some at the stern, but not as much.
Rolling is actually minimized the lower you go on a ship, it is simple physics. Picture a ship tipping side to side on its keel. The angle is the same on every floor, but you have more excursion from one side to the other the higher you go. So you spend more time "traveling" from left to right. The lower you go the less you feel the change in angle.
Add stabilizers and a ship in high seas may not roll at all, but it is still going to pitch.
Therefore, the best place on a ship is mid-ships and LOW decks. If you are on A-deck (the lowest crew deck) you will hardly feel a roll at all.