If you fell REALLY ambitious, You can modify void Main() so that it runs through everything twice: once for Autonomous, then again for user. The worse that could happen is that it screws with your controller and your robot self-destructs

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Serriously, the only thing you don't download over is eeprom, and that's not really used much (I think). If you just download the regular default code, it should work fine.
It would essentially create 2 programs. I would put Autonomous code in sepperate files.