How to upgrade new version of Eclipse instead of using new downloaded package?

In Window > Preferences: Install/Update > Available Software Site make sure that the Latest Eclipse Simultaneous Release (or Latest Eclipse Release) update site exists and is checked. Otherwise (in older versions or when this update site has been removed in newer versions), click Add..., enter the update site location https://download.eclipse.org/releases/latest and click OK.
Help > Check for Updates

See also Eclipse Wiki - FAQ How do I upgrade Eclipse IDE?

This might be useful.

https://wiki.eclipse.org/FAQ_How_do_I_upgrade_Eclipse_IDE%3F

There are some package structural changes from Eclipse Neon.

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