I built a professional project with AT89S53 and made a 10 pin header on the PCB for the atmel cable for serial programming.
I used the pony prog for downloading the software and I think it was good. Definitely not a joke.
During programming the reset pin of the microcontroller is held low so you have to read about the status of I/O pins when reset is active and design your drivers to be inactive when this state happens.
Regards
Mahmood