USB 3.0 ports work with the latest MultiBeast for El Capitan USB configuration options I listed in the installation procedures. I have not tested all of them as I don't have but one external USB 3.0 HDD case, and, I'm too lazy to test all the ports and headers.
I have tested my single USB 3.0 front panel port with a USB 3.0 thumb drive, and it works. (IIRC, I'm still using F_USB2 for my front panel as the F_USB1 header was reported a while ago as having problems.)
I'm now using Mac Pro 3,1 SysDef because I'm using a graphics card, and, for my purposes, the MacPro3,1 SysDef works fine.
My Thunderball system is still a good system to use, but it's taken a back seat to my Gene system, now.
Additionally, please provide complete details
in your Profile.
Mobo: motherboard manufacturer/model
CPU: detailed CPU model (e.g., i7-4770K)
Graphics: Video card manufacturer/model and/or Intel Integrated Graphics version (e.g., HD4600)
See my Profile items to the left of my post, under my name.
By doing completing your Profile and signature block, you help us help you better.