bootloader without usart?

I am wanting to use the usart for syncronous serial, but still be able to use the arduino development environment.

Is there a way to move the bootloader to use software serial on 2 other pins, since I will be using that in the code.

The other option is for me to hack some header pins or a switch to toggle between the USB serial converter connecting to the usart and the other pins, but that's something I would rather not have to mess around with between programming and running - hence the desire to talk bootloader out some other pins.