The source code for Protogame is available here: https://github.com/RedpointGames/Protogame
If you've started with a template and you want to be able to edit the source code, open up a terminal, cd to the directory where your project is, and then run:
Protobuild.exe --swap-to-source Protogame
then after saving everything in Visual Studio:
When the solution reloads you should see all of the Protogame source code there and you can edit it as you like.