Once you have created the firmware files you can deploy them using the Netduino.Updated / Deployment tool.
To start with I copy an existing piece of firmware in the tool. These are placed in directories with the board, firmware name / version.
Then edit the XML file in the directory to reflect the new version number you are using.
Now copy the files from the BuildOutput structure into the directory you have created overwriting the hex files in that directory (some renaming will be required).
Next up plug in the board in DFU mode (holding reset). At this point the board should be recognised by the update tools and you can flash your own firmware.
Hope this clarifies things,