SteelViking has words of power and truth. You will get a conflict warning any time a new mod rewrites a file already rewritten by a previous mod. It can be game-breaking or it can be as trivial as "XXX has already installed a file called 'readme'".
In SH3 I use Rik007's Recognition Manual, and I always install it last for what I think are obvious reasons. With JSGME I get a warning that some other big mod has already changed the .sil files for dozens of ships. Of course I tell it to go ahead, because those are the files I
want it to change.
There are three options.
1) Ask somebody here about the two (or more) mods in question. Of course that means you have to wait for an answer before you can play.
2) Learn to recognize files and know what they change. Of course this only works if you install, and re-install, and re-re-install a lot.
3) Memorize or write down what files JSGME says will be changed, and look for that specific change while you play. Of course that requires that you enjoy testing as much or more than you enjoy playing.
There are no easy answers, but there are answers. The downside is that JSGME sometimes puts you in that position. The upside is that JSGME tells you what's going on and lets you begin to understand what you can do about it.
I originally refused to use JSGME since I didn't understand it and it scared me. After reloading the game more times than I can remember I came to understand and love it. Now I've reached a point where I'm actually using other programs to go in and change parts of the actual mods. JSGME's 'warning' is for me just a reminder that I need to do something about some mod or other.
It grows on you.
