I ran Gentoo for years, and my experience was similar to yours. I could get things to work but it took a lot of frustrating trial and error, and then periodically a version upgrade would break everything and I'd get to start over. About a year and a half ago I finally got sick of it and installed Kubuntu.

Kubuntu 12.04 + 2 monitors + AMD proprietary drivers = you get to choose between accelerated OpenGL and multiple monitor support. You can't have both at the same time. (At least I couldn't, with the video card and driver versions I had 6 months ago. I spent many hours trying, then remembered I have more money than time and bought a $90 Nvidia card.)

Kubuntu 12.04 + 2 monitors + Nvidia proprietary drivers = easy. The GUI worked, first try, no problems. The only goofy thing was that my left monitor showed up on the right side, giving me a choice between physically moving the monitors or changing the default positions in the GUI. I changed the defaults in the GUI.

Also, on my former work machine, Kubuntu 11.04 and 12.04 + 2 Nvidia cards + 3 monitors = easy. (Some cow-orkers had 2 Nvidia cards and 4 monitors, also easy.)

I haven't tried newer versions of Kubuntu on a multi-monitor box, so it's possible (but not likely) they've gone backwards.