no easy way around this. oscommerce is really bad about upgrading to newer version. its best to install a new version, add your modules, design your template, and upload your db.
OsCommerce really does suck, I recommend getting a new shopping cart. Anyways, the best way would be to backup all of your files & MSQL databases. Then put your server offline and upload the new version, then test it and if you can't get everything back to normal you might want to pay a tech guy $50 to do it.