OK-I'm not a modder, but I have used JSGME a bit, so here goes:
When you get the message that a mod is overwriting some files from another mod, all that is telling you is that two mods (or more) are modifying the same files-not NECESSARILY the same parts of those files. (Although that is a possibility) Meaning, just because you get that message, doesn't mean that the two mods won't work together. It is just telling you that some of the same files are being modified twice. The only way you can really be sure is by trial and error; activate the mods, run the game, and see what happens. If things don't work right, (or don't work at all) exit the game, deactivate the mod(s), then try again. Often, there is a particular order in which mods need to be activated in order to have them all play nicely together.
Also, it is a good idea to use the "snapshot" function of JSGME to take a picture of your game files BEFORE adding any mods. That way, you can deactivate all mods, and compare your game files to the snapshot to determine if files have been modified to the point that you need to uninstall/reinstall your game and start from scratch.
Hope this helps, and I'm sure there are plenty of others here who can offer an even better explanation.
