Put the 2x3 pin ICSP header in - miso/mosi/sck/reset/vcc/gnd. That way you can plug an ISP programmer like usbasp or usbtinyisp In to easily program via ICSP. These are cheap, and much less of a pain to use than arduino as ISP, since just one connector, not a rats nest of jumpers
If planning to use bootloader and external serial adapter for programming, also do the 1x6 pin ftdi-style header.
Can copy ICSP from uno, ftdi from pro mini.