Hi there,
It would be best to setup a staging site and do the update from there so that the live site will not be affected in case there will be any issues with the update and you will be able to do some testing.
Here are some search results on how to setup a staging site:
https://goo.gl/8BkpJ3
In case you are not certain how to proceed, you might want to check with your web host and ask them if they can help you with the staging site.
Once the staging site is setup, you can do the updates from there.
As for the Visual Composer pages issue. Go to WPBakery Page Builder Settings > General and make sure "Legacy X Integration" is enabled. A common request we get is to not overwrite parts of the WPBakery Page Builder. We are committed to keep supporting sites from the early days of X where Visual Composer was our page builder but we’ve consolidated all that integration code under one setting. It used to be enabled by default, but you will now need to opt-in to use it.
Hope this helps.