MW cycling Newb question

Sort of. You'll end up with a marine tank setup for the bio-load of those mollies, nothing else. Given the time it will take to make the conversion, it would likely be faster to just set the tank up full marine, either cycle with uncured live rock, or with base rock/sand and cocktail shrimp, then introduce cycled rock.

A Protein skimmer functions by injecting very tiny air bubbles into the water column. The dissolved proteins in the water 'adhere' to the bubbles, and this froth is forced up a tube into a collection cup. It helps remove wastes from a system, improving water quality.

Mostly, that's true--a skimmer will remove beneficial stuff to, but not at the same rate, and it's better to get the sludge out than fret about trace elements that are easily replaced with regular water changes, IMO.

Water column refers to the water--as opposed to the substrate or other surfaces within the tank. Look at it this way--if you drop a rock into your tank, it's going to fall to the bottom, right? If you drop a pingpong ball in, it's going to float on the surface. But, if you add a cup of red dye, it's going to disperse through out the water--so, the dye is the only thing that is in the water column, even though the others are in the water.

Of course, I would not urge anyone to add dye to their tank. Just a visual example.

Essentially a Skimmer is used to remove protiens before they enter the nitrogen cycle, once they are in the Nitrogen cycle a skimmer wont work. The Nitrogen Cycle refers to organic protiens being broken down in Ammonia, and then broken down into nitrite, and then Broken down into Nitrate, and finally broken down into harmless Nitrogen Gas.