Dumb Bootloader and fuse question (you'll answer it in one post)

I've got a dumb question, and while I'm pretty sure I already know the answer, just want to double check.

I've burned code using a hardware programmer onto atmel chips before, and I know you set fuses to specific settings to get the code to run right. My question though, is that if I load a bootloader onto say, an atmega328 using arduino's "burn bootloader" function (even though it's not an arduino exact), once it sets the fuses, I will never have to touch the fuse settings again, and can just use arduino IDE to load new sketches onto the chip in the future, correct? I'm pretty sure I'm right, but i'm using QFN packages, so I can't exactly pop a chip off if I screw it up =)

yes, as long as the target circuit is compatible with the board you're choosing(speed, crystal vs internal oscillator etc.) you should be fine.

Obviously you're planning to have a serial connection so you can load new sketches, could you include a spot for a 6 pin isp connection?

bill2009: yes, as long as the target circuit is compatible with the board you're choosing(speed, crystal vs internal oscillator etc.) you should be fine.

Obviously you're planning to have a serial connection so you can load new sketches, could you include a spot for a 6 pin isp connection?

I've already got a 6pin header spot on the board, though it won't be populated (using an offset hole pattern to "lock" the pins to the walls when I plug a header in) to do initial programming. What I'm looking at doing is burning code once, and then facilitating user-upgradable code down the line (using USB connection through FTDI232RQ and the bootloader). My board is uno-ish, though only in the crystal/processor/header sense, but should work, my next task is to figure out how the arduino IDE loads code to the board so I can write my own firmware downloader