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Hi, Right now I am in the process of constructing all the input components for my project. I was wondering if using the Atmega64 with the bootloader allows installing the firmware via usb instead of using the db9 and db25 inputs? Or do you have to flash the PIC18F2550 via the db9 and db25 cables first, then you can flash the Atmega via usb?
Thanks for any help.

You have to use the db9 and db25 to make the parallel programming cable to do the initial programming of the chips. After that is done then you can do everything via the usb.

Thanks, I get it now.