The latest version of Notion is version 5.2.381. This version is fully compatible with El Capitan. If the automatic update is not working for you, please make sure that you are not connecting to the internet via a proxy server or vpn connnection. You may want to try connecting your computer to the internet via a hardwired connection if you are on a wireless router. You might also try turning off your firewall to isolate where the issue is. If you continue to have an issue, you may want to submit a support ticket at my.presonus.com under the Support tab. I just tested this functionality and the automatic updater is working on our end.
Should you ever need to manually update to the latest version, simply go to my.presonus.com and log into your account. You can download the latest version of Notion from My Products>Software>Notion.