The osCommerce upgrade is a hard and a time consuming task. Usually it requires manual files modifications.
The latest osCommerce versions include specific upgrade instructions in the "upgrade_guide.pdf" file for the installation package. Unfortunately the procedure varies depending on the current version of osCommerce you are running and different steps have to be accomplished.
We strongly recommend to create a backup of your website before you initiate the upgrade procedure. Detailed instructions on how to backup your osCommerce web site can be found here.