Hi,
To program a 9S08 MCU, it should be soldered on the production board.
To insert it in another socket, burn it, and then hoping that the MCU pins are still flat, is begging for trouble.
So the solution is to put the BDM connector on the board.
If the volumes are small, use a real connector, if it is large, use soldering pads where a special connector can be inserted.
For production, use eg the P&E Cyclone PRO, which can be used as a simple push-one-button-to- program equipment.
If you want to change the calibration value in the 9S08, (they are calibrated in the factory) check the AN2312. It talks about how to calibrate the internal oscillator on the HC908QY device, but it can be used for the 9S08 also.
Regards,
Ake