Programming Clock Fuses

I have a handful of raw ATMega328's (DIP package) with no bootloader on them. As I understand it, these come from the factory with the default timing source set to the internal 8MHz clock. My question is, when I program them with the Arduino IDE (using an Arduino as an ISP), does the IDE automatically change the fuses to set the timing source as the external 16Mhz crystal or does that have to be done manually?

If you burn the Uno bootloader as the first step, that will set the fuses correctly for future operations. You will need 16 MHz xtal, 22pF caps, and 10K reset pullup resistor connected at a minimum for correct operation after that. And select IUno as board type.

I am not loading the bootloader as I am migrating a couple of projects to permanent homes on Chibiduino boards and don't need it. So it sounds like I will need to manually set the clock fuses. Are there anything other fuse bits I should be concerned with like prescalers? I have already burned a couple of chips which have worked with simple sketches, but I didn't do any in-depth study to investigate whether their timing was accurate or not.

Digger: I am not loading the bootloader as I am migrating a couple of projects to permanent homes on Chibiduino boards and don't need it. So it sounds like I will need to manually set the clock fuses.

You don't have to use the bootloader. The first thing you upload via ISP will wipe it out anyway.

The "burn bootloader" command is just an easy way to set the fuses.

That sounds excellent. Thanks!