The deployment package is pre-compiled and contains no C# source code, its meant for use in production deployment. While it can be used in Visual Studio by opening it as a Web Site, that package is not really intended for development but for production deployment.
The source code download contains the Visual Studio Solution with all the projects and C# source code. Thats what I recommend developers use and this is what I use for development. Although I recommend you keep all custom work in your own custom projects and not modify existing mojoPortal code, there is a lot of benefit to working with the source code because you can find existing examples of how to do almost anything you would need to do by studying existing features. Seeing how the "Features" are organized into separate projects from the core in the source code package is also instructive for how you can organize your own custom projects to keep your custom code separate from mojoPortal.
Note that VS supports 2 kinds of web projects, Web Site Projects which have no .csproj file and just treat all files on disk as part of the project and Web Application Project type which does use .csproj files to determine which files are part of the project and all C# code gets compiled into dll in the/bin folder. mojoPortal source code is a Web Application Project not a Web Site project, so it works better in VS using the source code and the project files compared to using the pre-compiled deployment files and opening it as a Web Site Project.
Hope it helps,