My "new" system is about 8 months old. ASUS A5M99 R2 Pro, AMD FX-6300 6-core, 8GB DDR3 RAM, UEFI Bios, 2TB HDD.
After assembling the machine, first boot I hit the Delete to get to the BIOS. Went into Advanced and found the Secure Boot switch and turned it off. Used Gparted to partition the HDD with GPT and added in the EFIBios partition as first on the disc. The other partitions were basically for several distros and for each I had a /, /home, and swap. Multiple swaps are not necessary but I did it anyway.
No problems in getting it started. I have since added a 1TB HDD and a 128GB SDD, using GPT for all. On the SDD, I was careful to add "discard" to the options on the drive in /etc/fstab.
The only problem has been in getting the preferred boot order like I want it. As I added Mint 17 and later Ubuntu 14.04.1, each install adds an entry to the boot system. I am a distro junkie and this was annoying. I did find out via an article in LinuxBSDOS that the efibootmgr is the way to control the efi booting -- there is a man page for efibootmgr that is better than most man pages but read it all the way down to learn how to use things.
In setting up the machine, I did not see an option to toggle the IOMMU so I guess the default is ok. I have no trouble at all getting on the web.
Good luck with your build. Each manufacturer uses their own version of a graphical BIOS setter so you will have to figure out the one you eventually buy. You can usually find a copy of the install/owners manual for the motherboard at the manufacturers website. I have the paper copy for mine but I also have copies of the pdf version, including one stored in my Google Drive.