The problem with that approach is that every time you want to modify the program in your home-made board, you need to remove the microcontroller and put it in the programmer. Then move it back again before you can test the new program. You'll probably find that the program isn't quite right, so you modify the program and repeat the process a number of times. And you can't use SMD microcontrollers this way.It's more practical to put an ICSP header on the board and program/reprogram the chip in-situ.
How do you go about it?
Good use of rubber bands.