I like using a sharpie or a laser printer for individual pcbs, but double sided has to be lined up just right and all need lots of drilling/etc. So I usually use a prototype construction method, a-la
deadbug or
veloboard If you are just making a couple, that is the quickest/most cost effective route, or start with an arduino.
the veloboard version actually had a connector added for a bootloader controlled reflash/comm using rs232 or ftdi cable.