If you have access to the command line, you can upgrade the database non-intrusively. If you do not have access to the command line, you can run the database upgrade script from the web interface, but this will make your site briefly unavailable.
I strongly recommend copying your live website to a testing instance on a different webserver and performing any upgrades or new plugin installs there before rolling things out to your production website. This will also give you the benefit of seeing firsthand what the upgrade process looks like without affecting the production site.
If you installed the plugin through the web interface, the upgrade script has already run. If the information in the
versions database table looks ok, you do not need to re-run the upgrade script. If you manually copy a generic plugin into the filesystem, you will need to run (or re-run) the upgrade script. This will evaluate the whole OJS code for any needed database changes, and will perform them. So, yes, this affects the whole site, but it will only make changes as-needed in the database.
If using the web based script to run the upgrade,