I use the ATMEL ISP programmer and it allows me to change the "fuse" settings but it is tricky because the bit settings tend to stick. Have to read the bits, then clear them, then write the new settings back to the MCU 5 or 10 times before the bits are reset. Finally, when the bits read what I want, I can program the flash memory with the software.

Tried programming the same MCU with my SuperPro 3000U programmer and it automatically set the two lock bits every time - no way to clear the bits before programming - they always locked to the on position.

So I recommend that you use the ATMEL ISP programmer if you have a parallel port on your computer (USB version said to be flakey) and add the 10 pin programming header to your project to access the ISP pins directly. Simply plug the ISP programming cable onto the header to program the project.

I keep one board, with the 10 pin header, at the shop and program the MCU's with that, then put the programmed MCU's into other project boards and don't have a header on those.