Templates and override files do not get overwritten when used correctly ... that is the point of your personal overrides directory ...

As to changes needed for them, get something like Beyond Compare from scootersoftware.com

This let's you compare a clean old zencart to a clean new zencart to see differences ... this will show you full differences between 2 versions ...

You can also compare clean new zencart to your override files to see the differences, if any, more readily that might affect your files ...

If you never touched a file, and never made an override for it, then the files just will work on their own without any changes on your part ...

The upgrade of the database is managed by the /zc_install on the Upgrade Database ...

It is a good idea to upgrade a test directory and copy of your database first to see if you will run into any issues that might require tweaking to the files ...

Backing up both your site and database prior to any kind of upgrade is important ...