lavertyg, I have spent the most part of the last 3 days experimenting and have finally got El Capitan to boot from my P8H61-M Pro board using UEFI boot. It took a combination of things to get there, but I think the key thing was to replace the OsxAptioFix2Drv-64.efi driver with OsxAptioFixDrv-64.efi.
With my setup I also needed to add dart=0 to the boot flags. I also had the AppleRTC, AsusAICPUPM and KernelPm patches set. The autodetection for my Nvidia Graphics card reported 2 ports whereas my card has 3 so I changed this to 3. Since I had also created a clean EFI on my OSX HDD using the latest Clover installer, I found that it was important to have NullCPUPowerManagement.kext and FakeSMC.kext in EFI/CLOVER/kexts. It wouldn't boot without them. I also needed RealtekRTL8111.kext to get the network adapter working.
Of course, the USB drive installer already has these kexts, so once I had finished experimenting, I just copied OsxAptioFixDrv-64.efi into Drivers64UEFI and renamed OsxAptioFix2Drv-64.efi. UEFI booting now works from the USB stick.
At this point I still haven't got it booting my Windows partitions though but at least I can now boot both Yosemite and El Capitan via UEFI with Clover.