For barebones systems, unless you need to use the serial monitor or have it communicate with the PC for some other reason, I think it's easier to include a 6-pin ICSP header on your board and program it via ICSP instead. You can even use your Arduino as the ICSP. See Prototyping small embedded projects with Arduino | David Crocker's Solutions blog. To install a 6-pin header on veroboard you need to cut 3 of the strips between holes, but this isn't difficult with a sharp knife.