Stems usually have some amount of rise, usually a few degrees (they aren't perfectly straight.) Flipping it means literally flipping it from the stock position (which is usually the relaxed position where it raises the bars) to the position where it lowers the bars. Slamming the stem is removing all of the spacers from between the stem and the headset and putting it in the lowest position possible. It does usually make your position more aerodynamic, and yes, less comfortable. Once you're comfortable on a bike though, you can make adjustments like that with it still being rideable.

And Aeolis, watts are simply the SI unit for measuring power. When you're pedaling a bike, you're producing power, and buying a power meter to monitor your output is one of the best ways to train.