bare-bones X versus enhanced window managers

[paradigm-X]

One thing that is not clear to me yet is the relationship or interplay between the bare bones X configuration settings, which one might, for example, put into various files in '/etc/X11/xorg.conf.d/', such as '10-monitor.conf', and the effects these would have on window elements when there is also another window manager in place, such as XFCE, with its own set of applications to control windows and other programs. I mean, for instance, since I have installed XFCE on Gentoo with Virt-Manager in KVM/Qemu, Is there any point in then fiddling around with the X config files to tweak the display and behavior of input devices, or should I be trying to tweak these components using the programs made for XFCE to do so? In other words, where does the line of control end with X and begin with XFCE and such?