Once a bootloader is burned onto a microchip (atmega 328) can you just plug it in to the Arduino, do all the programming and such there, then pop it out and place it into your device, ready to go?
Or do you have to use a seperate circuit to program the chip, using Arduino as ISP (This is what I've been doing)
Once a bootloader is burned onto a microchip (atmega 328) can you just plug it in to the Arduino, do all the programming and such there, then pop it out and place it into your device, ready to go?
Yep, ain't it great. 
Just make sure your circuit has the right support parts for fuses & stuff you have set - for example, 22pF caps/xtal if running at 16 MHz.