Agency Partner for WP is the one described here: it sells our catalogue through your Agency space. The older Partner plugin talks straight to a reseller account of your own at the provider and is a different arrangement. Backup Toolkit and the security plugins do their own jobs and need no account with us at all.
From the WordPress plugins page on this site, which lists each one with the commands to fetch it and verify its checksum. The figures there are measured from the published release rather than typed by hand, which is what makes checking them worth doing.
Fetch the current release and unpack it over the folder, or pull it if you installed with git. Your settings survive an update — they are stored in WordPress, not in the plugin folder. Deactivating a plugin keeps them too; only uninstalling removes them.