Not normally. Usually if there is a conflict in the settings it will give you a warning box with 4 options. If you select a certain option it might break your existing config, but then the message for that option says that.
If you like, for your organisation. It is not necessary though. If it was a different game, I tend to keep the configs in separate files, but that is because they can end up getting large as it is, and there is nothing worse than breaking a working config because you were trying to change settings for a different game. That said, you can have different game configs in the same file too and they can all work, despite some of them being different styles of setup e.g. D3 and WoW are different styles.
Not offhand. Are you sure it is not in game bindings or some other addon causing the issue? Perhaps if you shared your ISBoxer profile it would be possible to determine whether the issue was with that.
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