I'm not a Fedora user, so correct me whenever I'm wrong..but here goes:
Yumex being a graphical front-end to yum means that the program that does the real work is yum, but you control yum trough Yumex. So it's basically just the same thing as if you used yum (from command line), but you just get a "nicer" way of controlling it than typing commands. It won't harm any update/installation things, unless you're doing something that would break things, and in that case it's still the same as if you used yum. Using yum = using yumex, the only difference being the outlooks of the controlling interface (you clicking a button vs. you pressing ENTER).
I didn't quite get the last line, Yumex is a program, not a reposity. Livna is a reposity (isn't it?), and nevertheless you configure Yum reposities in a configuration file, which can be edited using a text editor, or if the graphical interface allows you to, trough it. Still it doesn't matter which one you use - one configuration for yum, and Yumex means using yum graphically, so it's the same configuration.