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I am putting together a couple of projects with my own board design, I originally intended to use a atmega328 however I have decided instead to go with the atmega2560, the 328 actually gives me all the digital and analogue pins that I need however I need at least 2 proper uart ports for my projects so although the majority of the 2560 IO pins will be unused it will give me the most flexibility for my serial devices.

I need to run my projects at 3.3v and so therefore 8Mhz, I understand this will be fine for the 2560.  I am currently designing my board and will include an external 8Mhz resonator and programming header.  Is there anything I need to consider for burning the bootloader onto a blank chip when it is on my completed board? in the past I have found with the 328 DIP chip that I have had to hook up a 16Mhz clock to be able to burn the 8Mhz bootloader, obviously my board will be smd so it will not be possible to swap resonators just to program the chip.

I also need some guidance on how to prepare a 8Mhz bootloader and board config for the 2560 at 8Mhz, to be honest I don't fully understand the ins and outs of bootloader and programmer config yet, I am still trying to find a good all-round guide.

Will I be able to use an arduino as ISP for burning the bootloader to the 2560?