These are the recommended steps for upgrading Onpub to a new release:

1. Download the latest version of Onpub
2. Rename your old Onpub install directory to onpub-old
3. Unzip the new Onpub download in the same parent directory as onpub-old
4. Copy the contents of your onpub-old/local directory to your new onpub/local directory
5. Copy any other files you customized outside of the local directory to the same directory under the new onpub install directory
6. Login to the new version of Onpub and verify that everything works as you expected
7. Delete the onpub-old directory to remove the old version of Onpub

That is pretty much all there is to it. Since all customizations to your Onpub frontend live within the onpub/local directory, it's enough to copy the contents of this directory to your new install in order to upgrade. This allows you to easily keep your local customizations, while also taking advantage of core improvements to the application inlcuded with each new release.