If you want to save your edits to the source code, you have to edit it within the SGDK2 IDE, or edit it in Visual Studio and then copy your edits into the proper file in the SGDK2 project's SourceCode folder in the IDE. Each time the game is compiled, all the files in the generated project folder are overwritten by content that is generated based on the SGDK2 file. However, if you happen to be editing code that is not contained in the source code folder in SGDK2 (because it's one of the few bits that are hard-coded into the code generator) then yes, your only choice is to load the project into Visual Studio and edit it there. Of course the you can never compile your project in SGDK2 again without overwriting what you did... you would have to re-apply your changes every time you compile from SGDK2.
On the topic of screen size, though, I noticed an interesting thing while working on my OpenGL test program. It's really easy to make the screen resizable and have the contents stretch to fill the window. Maybe I'll allow that in 2.1 instead of making the window a fixed size. Also, it'd be kinda cool to be able to zoom out in the map editor! I could really open up control over sizes and aspect ratio. You could define any size screen that you want to work with, and then if it doesn't fit the display, it can just be scaled. I suppose I'll need two sizes: Game Size for defining how much graphics you want to fit on the screen (640x480 pixels worth for example), and Viewport size for defining how big it should be displayed (by default). Viewport will change as the window size changes, and will have to fit a full screen resolution if the player switches to full screen (though that's not supported in OpenTK yet). I wonder if there's a better term for "Game Size".
BTW, I'm thinking full screen is not such a necessary feature... do many people find that important? I suppose it might improve performance in some environments, but ideally, I think a lot of people like to play within a window.
Ooh, I think "Native Size" might be a good term instead of "Game Size"