Hi,
The thing to understand is that all the code has to be compiled by visual studio and that compilation results in the dll files in the bin folder.
The dlls produced by VS are basically the source code compiled to msil (microsoft intermediate language I think that stands for).
The ASP.NET compiler then further compiles the dlls and the .ascx, ,aspx files etc into native instructions for the given processor of the machine. Those files live down under windows folder in the temporary folder for asp.net files. So the code you compile in VS is portable to any machine but is then compiled for that machine by the asp.net compiler.
So if you make changes in the source you must recompile in VS and then re-deploy, the updated dlls and other modified files (.aspx .ascx etc).
The best thing to do is remove your custom code from mojoPortal projects and refactor it into separate projects of your own so that is is not compiled into the mojoPortal dlls by VS.
Hope that helps,
Joe