In my limited experience, HEC1 does not calculate 100-year elevations, but merely 100-year flows. It does this based on SCS curve numbers and stream channel characteristics. Depending on the size of your stream's drainage basin, this could be incredibly cumbersome, or just cumbersome. For smaller drainage basins, I use the SCS Curve Number method and HydraFlow to calculate my 100-year flow, while for larger drainage basins (measured in square miles, not acres), I use USGS Regression Equations.
I have no experience with HEC2, other than everyone saying: "So you escaped that nightmare, aren't you lucky?" HEC-RAS is the software you'll want to use to determine the 100-year elevation.
HEC1 is grotesquely outdated. Its input and output is text-based, with data fields refered to as "cards", and my first experience with HEC1 output left me with a 64,000-page output file. I would recommend that you give it a big swerve.
I recommend that you look at FEMA guidelines for their studies as a basis for your methodology.