I've just finished a new build for a friend
Z97-A
i7 4790
16 gb ram
evga GT740
samsung ssd 840pro
1tb second hard disk
Thunderbolt Ex expansion on the last Pci-ex at the bottom of the mainboard
I've installed win 8 on the tera disk making a little partition of 50gb.
I've installed the asus drivers for audio, lan, sata, chipset and the thunderbolt ex expansion
I've shut down the pc and attached the Apollo audio interface via thunderbolt cable.
I changed the thunderbolt bios security settings to ask to approve when the tb were connected.
Restarted to windows and, bang, it asked me to approve the connection on the thunderbolt. Approve, shut down.
Then I unplugged the tera disk with windows and plugged in the ssd. I also unplugged the audio interface.
Unibeast usb with El capitan. Installed osx and rebooted using the usb as boot disk, nv_disable=1in clover boot options (without it i had a spinning circle on black screen), configured osx and reached the deskotp.
I used multibeast, with those settings:
Uefi boot
Audio: Realtek ALC892
Disk:3rd party sata
Misc:FakeSMC, with plugins and hardware monitor.
Network:intel-AppleIntelE1000
System Definition:MacPro3,1
Rebooted, this time from ssd uefi, nv_disable=1 again, reached the desktop, downloaded the 10.11.3 combo update and started it.
After the Reboot, nv_disable=1, I reached the desktop, downloaded the nvidia web drivers for 10.11.3 and installed it, the I selected the nvidia drivers from system preferences. I also installed the UAD audio drivers (Apollo thunderbolt) and Shut down.
I plugged the Apollo thunderbolt, i've started the pc, this time without nv_disable=1 using the nvidia drivers.
Reached the desktop with full functioning system with working sleep/wake, just some random usb issues i solved reading the usb fix topic for El Capitan.
The UAD Apollo TB is working really good with Logic X and 64bit plugins...
I use an Asus N13 wifi dongle with his own Mac drivers and an Asus BT400 bluetooth dongle working OTB for a magic mouse.
that's it.