PIC16: How do I modify the configuration words?
It has to be done by the programmer (technically this is what the PICKIT 3 is, not a bootloader).

You can configure the configuration words from MPLAB, or by inserting "#pragma config" statements into your C code. This is preferable, as it ends up checked into source control and doesn't get lost.

http://www.kwantlen.ca/science/physics/engineering/APSC1299/files_for_lab/pragma_config.html 

You cannot modify the configuration words from within a PIC program.