The upgrade process itself shouldn't be trying to add those email templates again, but from this post
it looks like there's already duplicate data in the database (probably from earlier failed upgrade attempts). For each of the duplicate templates listed there, remove one of them. The part of the upgrade process that's failing is the creation of a unique index, which will result in an error if there are any duplicate errors.
(FYI, if you encounter an error on upgrade, it means your database may be left in an intermediate state between the two versions; whenever that happens, it's best to restore your database from a backup made before the upgrade was executed, correct the issue that caused the failure, and continue from there.)
There was previously a "manual install" option, but some of the database entry process was moved to PHP rather than pure SQL, so we removed the manual install option.
The "create database" checkbox causes OJS to attempt to begin with an SQL "CREATE DATABASE" statement; regardless, the installation procedure is intended for execution only on an empty (or non-existent) database. Whenever you have a database with existing OJS tables, you must use the upgrade link instead.
Public Knowledge Project Team