My Mac Pro (early 2008) is behaving itself finally (after months of not working properly with El Capitan) with the latest round of updates from both Nvidia for its driver and El Capitan from Apple. ((MacOS 10.11.3) and the Nvidia driver (346.03.05f01)
Previously, I had an Apple-ROM-flashed ATI Radeon HD 5770, and experimented with an additional Geforce GTX 750Ti (stock PC), which both resulted in sporadic logouts when I upgraded to El Capitan from Yosemite, although it became fairly stable by turning off the "Displays have separate spaces" functionality, although the system got non-fatal errors browsing within many applications' file opening dialog boxes...which I have been sending off to Apple, using the built-in crash reporting functionality within MacOS with Xcode installed.
Perhaps a factor in getting things working smoothly is that I decided to stop mixing card types - now I've only got Nvidia in the machine - it's currently got a Nvidia GeForce GTX 750Ti running two Apple Cinema 23 inch displays, and an old Nvidia GeForce GT 240 running a third. Both cards are standard PC cards, no flashing with Apple ROMS - these aren't "mac" cards.
I find it's good to have the older card in there, because I have found that the new GTX 750 displays nothing at all with the built-in Apple drivers in El Capitan. The GT 240, although it doesn't display the boot screen (as can be expected), once the OS loads, works fine in El Capitan without the Nvidia driver, whereas both cards would display video in Yosemite without the Nvidia driver.)
Happily working on all three cinema displays on my Mac Pro with "Displays have Separate Spaces", which I love, working fine now!