I do not use a boot-loader and the programmers I use are the PICSTART PLUS or PICKIT2 and mostly MPLAB, so this may not be of use to you.

I set the fuses in the *.inc file. I have found that once the fuses are set for the chip I do not change them often. But that is me. I will make a note in the code of how the fuses are set.

I know...why not set the fuses in the code if I make a note of how the *.inc is set in the code. For me it just seems to work better.