I am using a digistump board. The bootloader is loaded from an Arduino Uno with SPI. I can't find settings for the clockspeed here so assume it's default 1kHz.
I program with Arduino IDE. With digistump board attached to USB. I can sellect 1 - 8 - 16 mHz. It's done by plug in and plug out of the USB. It's not connected the whole time.