It took me a while to figure this out (even with provided documentation in the forums here).
But here is the steps that I take:
Take note of this file: /usr/share/kibana/src/ui/public/images/kibana.svg
*** This file is your corporate logo template. I used the Inkspace app to edit it, add in our corporate logo, etc.
Make a backup of it. Note: This logo svg will be replaced automatically between updates/upgrades of Kibana - every time. Remember this.
Once you have your edited SVG ready to go, copy it back to /usr/share/kibana/src/ui/public/images/kibana.svg (overwrite the file).
Stop the Kibana service.
Install a Kibana plugin, such as X-Pack. Example:
/usr/share/kibana/bin/kibana-plugin install x-pack
Wait for the "Optimizing and caching browser bundles" process to complete. This can take a while, up to 20 minutes.
When done, start Kibana and log in. Verify the logo is set up to your liking.
Wash, rinse, repeat on other Kibana nodes (if applicable).
Optional: If you aren't licensed for X-Pack, buy a subscription Otherwise stop the Kibana service, remove the X-Pack plugin
/usr/share/kibana/bin/kibana-plugin install x-pack, then start Kibana.
*The optimization process only runs when you install a plugin, not when you remove one.
This process works for me in Kibana v5.x versions as well as 6.0 and 6.1. Things may change in 6.2 though....
I'm not sure how to change the browser favicon yet. Personally, I'm ok with the Kibana favicon so it is low priority for me to figure out how to get that swapped out with my corp icon.