Here's how I kept root AND CWM RECOVERY. I did use the built-in function in SuperSU. I am pretty sure you must use the PRO (payed) version if you want this functionality in SuperSU.
So, if you have SuperSU PRO, you should load the update .zip file via recovery, and not do it over the air (OTA). After the zip is installed but before the reboot, SuperSU will ask you if you want to protect your recovery partition (say yes), and restore/protect root (say yes). Reboot and you're good to go. Root and recovery are maintained!
Looks like OTA Rootkeeper also successfully kept a copy of root, so that likely works too (I didn't test this method, but instead used the SuperSU method outlined above). I have no idea if the update would have rewritten recovery back to stock, but using the SuperSU PRO, I didn't have to worry about that possibility. Neall