Simple answer is that you can use whatever method/application you feel comfortable with.
AutoCAD, Revit, Max, Maya, and SketchUp are some desktop-based applications that one could use. AutoCAD and Max have native STL export (which is what Makerware can open). Revit, Maya, and Sketchup have plugins. For Revit, download it from Autodesk Exchange. For Maya, check out this post. For Sketchup, install the extension.