Do you have ArcGIS Desktop 9.3, or 9.3.1? The ArcHydroTools9.msi installer (build 1.4.0.258, Jan 9 2013) on the secure download site will install and run for either release of ArcGIS.
Once you install, the ArcHydro Tools Help article will take you through the map algebra processes ArcHydro Tools perform for conditioning the DEM (filling sinks), and identifying flow direction, flow accumulation, stream network and/or basin, and finally raster to feature conversion.
Also, the ArcGIS 9.3/9.3.1 Spatial Analyst help, has some guidance. But is a bit disjointed and out of sequence compared to the Help presentation in ArcHydro Tools, and be sure to review the "Learn more about..." Help panels as well. It will work, but the data handling is a bit more demanding when using Spatial Analyst extension compared to ArcHydro Tools.
