Bartender 2 has just been released, it's fully compatible with OS X El Capitan and does not need the below steps performed.
We recommend all users should upgrade to Bartender 2.
OS X El Capitan introduced a new Security Feature called System Integrity Protection. With System Integrity Protection Bartender 1 needs additional setup steps performed before it can control Apple menu bar items such as Notification Center, Battery, WiFi etc. Bartender 1 can still control menu bar apps fine, without these additional steps.
Unfortunately we cannot automate all of the setup and Bartender 1 will need you to temporarily disable System Integrity Protection to allow it to install its System Item control component, System integrity Protection can then be re-enabled.
Apple have made the steps to temporarily disable SIP quite difficult, so we now recommend only performing these steps if you really must control Apple Menu Items with Bartender 1
Please follow the instructions below to allow Bartender 1 to control System Items.
(You may wish to print these instructions or open them on another device as you will be restarting OS X).
First you will need to Reboot into OS X's Recovery Mode to Disable System Integrity Protection, to do this:
You can now re-enable System Integrity Protection, to do this:
Congratulations, Bartender 1 can now control System Items and System Integrity Protection is enabled.