I use either a USB to TTL converter cable with a PL2303HX chip built into it ( available on ebay ), or a converter using the ATmega16u2, built with the design from the schematic of an arduino, and programmed with arduino DFU firmware.
The converter allows programming the 1284p through the serial UART on the chip, using the "optiboot" bootloader burned onto the ATmega1284p.
The bootloader firmware was downloaded from the "maniacbug 1284p project" on the web.
The bootloader would be loaded on the chip with the AVR-MKII programmer.
Once loaded, a bootloader provides an alternative to using the AVR-MKII SPI programmer.