If you have any warning with JSGME then
don't enable the mod! it basically means that a file already exists from a previous mod that has been enabled.
What you should do is merge the files externally copying the newer files to the older ones, however with cfg files it is better to edit the one adding all data to the new, especially with files like
EnglishNames.cfg,
locations.cfg for example the EnglishNames has to be edited for each ship being installed or you will end up with CTD, the
Campaign_Lnd.mis file contains the land based (cities etc) for the campaign your running, the replaced one has to contain the old information
plus any new information on the new mis file being enabled, or the location will not exist, this will also explain the
Locations.cfg file!
Give a list of the existing mods that are enabled (just the ones that will conflict), and the new one that causes the conflict, we can then determine what to do from there, eg:
This mod conflicts with
that mod.