There are some mods which are intended to be installed in SH3 Commander, which Commander then uses to modify the SH3 game files at load time. WB's Warning Orders and WB's Mid-patrol Radio Orders, for instance, both have SH3-Commander versions. The cool thing is that mods installed through Commander can be time-specific - only apply during June to October, 1942, for example. But the mods have to be written to work that way. As Steve said, just putting a Mods folder into Commander won't do it. Mods intended to be activated in SH3 Commander will tell you so in the documentation. All other mods should be activated through JSGME in the normal way.
IIRC, there are some brief - and not entirely correct - words in the Commander documentation about how to do time-specific and random mods.
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