You are looking at the Netduino as a remote storage device and this is not what the Netduino is. When the Netduino is powered, the application stored on the Netduino is running. If the app is written to run in loop mode it continues to execute without end. If there is no loop the application will run when powered up and run to it's end.
You can run something like the NeonMika web server on the Netduino which will host a webpage that a user can access via the Netduino's IP or NetBios name. This web application can then allow a user to make changes on the webpage and submit the pages which use jquery and .NET to receive and store the settings and update the settings.xml file.
I am not sure what exactly you are looking to accomplish, but this sounds like the solution you may be looking for.
Dave, Question, I'm running the latest firmware on my ND Plus 2, The Mika webserver doesn't seem to work out of the box for me, lots of build errors. Do you know of any examples or references that have actual working examples for the Mika webserver?