I've done a lot of testing around this.
BIOS mode will result in very slow SSD performance with high CPU usage as the drive controller will be ATA mode. AHCI is not available on the Mac Pro when Windows is installed in BIOS mode.
If you have a Samsung XP941 SSD and a GTX 680ME you must use BIOS mode otherwise you will get no image on screen once you've installed the NVIDIA drivers. This is a GTX 680ME specific issue.
If you have a Samsung SM951 SSD you can run Windows fine in UEFI mode with a GTX 680ME and it will be using an AHCI controller hence running at full speed.
Summary: If you need BootCamp and have a GTX 680ME then get a SM951 SSD.
As for the mention of long boot time when using UEFI, I don't seem to be affected by that.
You can check which mode you've installed Windows in after the fact by running the command msinfo32 (14th line down)
[doublepost=1484328705][/doublepost]As for how to do it...
The easiest, if albeit slower, way is to burn the Windows ISO to a DVD.
Hold down the option key and select to boot from the left option for BIOS mode or the right option for UEFI mode.
(sorry can't remember the exact names it lists. I think one says EFI)
FLASH DRIVE:
If you want to install Windows in UEFI mode, you can use RUFUS (Windows app) to create a bootable UEFI Windows flash drive. Ensure the USB flash drive is using FAT32 and not NTFS, and install the ISO to the flash drive using Rufus. Then, assuming your Mac is a 5,1, boot off the flash drive.