With new construction, sheetrock is usually put up horizontally,
which means there will be a beveled edge along the floor where
the baseboard molding goes. How do I keep the molding flat with
the wall if it's nailed against the bevel on the sheet rock?

We use 5 1/2" baseboard. If you' re using 2 1/4 "casing", I suppose you
could ask the drywall guy to run his knife/mud along the bottom edge