I don't recommend adding files into the mojoPortal.Web project because then your code is compiled into mojoPortal.Web.dll. If you later upgrade to a new release the dlls will be replaced and your code will be lost.
Even if a control inherits from SiteModuleControl it still has a code behind that is compiled into a dll. It is possible to make a control using inline code instead of codebehind and that will not have a dll and code changes will take place immediately without needing to build, but anytime there is a codebehind .cs files they must be compiled. mojoPortal uses Web Application Project type where all C# code is compiled into dlls in the /bin folder, we don't deploy source code to the production server. There exists also a Web Site Project type in VS that is not used by mojoPortal, in a web site project the source code is deployed and is compiled on demand by the asp.net runtime.
If you want to use inline code you should not copy any module form mojoPortal because mojoPortal is not using inline code. Our hello world examples use inline code, you should use that instead. However for more advanced features I recommend use custom web application projects for your features with codebehind and post build events. You can learn how to do that from our series of videos that walks through building a simple guest book feature.
See also Avoid Forking the Code.
Hope that helps,