For the latest 10.11.5 here is the recommended upgrade procedure. There are no known compatibility issues at this time for upgrading directly from the AppStore.
Download and Install the update from the AppStore. Allow your machine to restart.
In clover, change your boot options to set
Boot. Allow the update to continue and wait for it to install. If you’re using -v boot flag don’t expect to see the normal progress indicator however the update will install in the background so be patient.
Once booted – download the latest NVIDIA Drivers. Reboot after installing and use the standard