Guess this is widely published on the web but since I was searching for this like mad today I have to write it down for the next time I need it.
In order to enable the Eclipse update manager UI in Lotus Notes:
- Close you Lotus Notes client
- Browse to the plugin_customization.ini in the notes application folder\framework\rcp
- Add com.ibm.notes.branding/enable.update.ui=true
- Save and close file and restart Lotus Notes
You can now find the Eclipse update manager under File > Application > Application Management.