Here is a quick guide to enable onboard audio on your X99 system. (Confirmed working on my Asus X99-E WS motherboard running macOS 10.12.2 and Realtek ALC1150 codec)
We will be utilizing the AppleALC.kext injection method via vit9696.
1. Set up audio injection on Clover
The number in the Audio Inject menu should be the profile you want, in my case profile 1. Supported profiles are found here for your codec. Save your settings.
2. Download compiled AppleALC.kext
3. Install AppleALC.kext
Copy the AppleALC.kext file to your /EFI/Clover/kexts/10.12 folder.
4. Reboot and test.
Use the green audio plug if available. Ensure "Internal Audio" is selected on your audio output settings.
Once selected, you can switch between alert sound effects to test your audio.
Feel free to post any questions.