If you’re not using gnome or xfce but have some gtk apps installed then you could always set your theme preferences via ~/.gtkrc-2.0 like this:

~/.gtkrc-2.0

gtk-can-change-accels = 1

gtk-icon-theme-name = "Faenza-Dark"
gtk-theme-name = "Zukitwo"

style "user-font"
{
        font_name="Terminus 12"
}
widget_class "*" style "user-font"
gtk-font-name = "Terminus 12"

But with gtk 3.0 this changed. You know have to edit the file ~/.config/gtk-3.0/settings.ini which will look like this:

[Settings]
gtk-application-prefer-dark-theme = false
gtk-theme-name = Zukitwo
gtk-fallback-icon-theme = gnome
gtk-icon-theme-name = Faenza-Dark
gtk-font-name = Terminus 12

To avoid visual differences you should choose the same (if possible) or a similar theme for gtk3 and gtk2.