What you are doing with the SA tools is the same thing that Arc Hydro does. Arc Hydro is an ESRI product free for the downloading. If you are doing a one-time project, the muscling it through SA is fine. If you will do this again and again, then you may get and learn Arc Hydro. Everything that Arc Hydro does I believe you can do with SA. However, Arc Hydro goes way beyond the simple tasks.
The concept is simple. Start with a raw DEM, "burn in the streams" using polylines for the drainage system or streams. Convert the stream layer to a raster with a big value and subtract that from the DEM. You can burn this deep, real deep. The next thing to do is to "build walls". Here you create a raster from a "wall" polyline or polygon using a big value. Then you have to "breach" the wall using the stream raster. Then add the results to the DEM. This raises the DEM where you need the flows not to cross. You need this to be at least 2 cells wide or the flow will "sneak" through the corners. After this is done you need to fill sinks. If you don't fill sinks, when you do the flow direction, some will end in the sinks and not where you want the flows to go. Once the flow direction is final, then the rest of the watershed analysis should go smoothly. There are occasional situations where you need to revise the flow direction (adjust flow direction with streams in Arc Hydro), but I find this to be a rare occasion. Good to be aware of it though. Arc Hydro has a flow trace tool that would make it worth installing Arc Hydro anyway. It allows you to click on a cell and see which way the flow direction goes.
Since this is process is always iterative for me, I use model builder so that I can easily rerun the process as I make minor corrections in the stream polylines or wall polyline. Arc Hydro comes with some ready-made model builder tools and workflows. I copy and modify these for my use.
There is a Arc Hydro discussion group where you can get help from the community. I created a discussion in that forum a while back called ArcHydro Problem Solvers. If you want to try using Arc Hydro, it might be worth perusing that discussion.