Best way to work between a staging and live site, without overwriting member

When I work on our staging site, time goes by, and I'm always scared I'm going
to overwrite member data, activity posts etc.
What's the best way to update your site without doing this?
In our host Cloudways, there's an option to select which database tables to
If I wanted to update my site, make sure all the plugins are up to date and dev
work, without effecting anything on the site, does anyone know what options to
select here?
Just web applications, or would there be other tables I should update / avoid

Originally posted by George Fourie on Facebook