I start with a base flange feature, either the primary profile of the part or the primary face. Then add edge flanges or other features using the sheet metal tools. Many of the needed hole features can be included in the edge flanges and remain well behaved when revising material, thickness, bend radii, etc. My back ground is primarily sheet metal fabrication so the SW tools makes sense functionally, and I have been modelling sheet metal in SW for 17 years. The software tools are robust when used as intended. If you find yourself having to add too many steps in the feature tree, or lookind for work-rounds you may want to review the help files for the sheet metal tools. I'm in that same situation when working with swoopy parts using surfaces, having to go back and review the standard tools and not add features just to tweak something.
Diego