The SmartStore.NET package with source code contains the ClickToBuild.cmd batch file, which will deploy everything correctly for you to a "Stage" folder. The build process will build the project in release mode and move all compiled and deployable files to the correct directory: build/Web.
SmartStore.NET source code distribution does NOT contain the NuGet packages required to build the solution successfully . Instead, these packages are downloaded during the very first compilation. Thus, when your initial build attempt fails, this could indicate that the packages could not yet be downloaded completely. In this case, just build again! If you're still getting errors, try to compile the solution in Visual Studio 2013 before running the .bat file, but make sure beforehand that SmartStore.Web is set as your startup project.
After a successful build, select all the files in the build\Web directory and upload them to your web server.