Well, I set the fuses like so the first time because I was having trouble getting it to program (the IDE hides the option to upload with a programmer so even though I had a programmer selected I was getting com port errors and didn't know why until I figured out the right upload option was on the fil emenu):http://www.frank-zhao.com/fusecalc/fusecalc.php?chip=atmega1284p&LOW=CE&HIGH=F9&EXTENDED=FF&LOCKBIT=FF
But the boards.txt file has the following fuses:http://www.frank-zhao.com/fusecalc/fusecalc.php?chip=atmega1284p&LOW=FF&HIGH=DE&EXTENDED=FD&LOCKBIT=FF
I'm not sure if they get programmed though because a couple weeks ago I had a chip on a breadboard that was running slow and I was using the same boards.txt and the right chip selected on the menu. So I don't think it was being programmed to use my external oscillator. But the current chip is running at the right speed, going by the fact that my led now blinks once a second like it's supposed to.
Other than that, I just select upload via programmer from the file menu, and I have usbtiny seleced for programmer and avr-developers.com selected as the board for my 1284p.
The thing about one computer programming faster than the other was with 328P's. I haven't tried it with this chip; I don't have time to mess around with that right now I gotta get this board working pronto and the slow programming is only a minor inconvenience.