You can develop against the pre-compiled deployment files of mojoPortal if you don't want to work with the source code.
However I think you then miss out on the benefits of having easy to find and read code examples for almost anything you want to do.
I don't recommend you add files to the mojoportal projects and compile your stuff into the mojoPortal dlls at all.
I recommend you create your own projects in the solution in a similar fashion to how we have orgasnized the mojoPortal.Features projects and the WebStore projects keeping all the code for those projects separate from the core and using post build events to copy the output up to the Web project for runtime.
Hope it helps,
Joe