For some time now, I’ve been using x2x to combine two X servers to one virtual workspace. It’s nice, because you can move your mouse off the display (say, your desktop machine) to the X server of another computer (in my use case: my laptop), and continue typing and clicking with your main mouse/keyboard. However, x2x gave me a few headaches, since the copypasting (middle mouse button) would not always work correctly between the two monitor setup you get.
However, I found out that synergy does the right thing when it comes to copypasting, so I switched to using synergy instead of x2x, and if you’re seeing the same problems with x2x, I can only recommend trying synergy. Most likely it should “just work” for you, too.