[Murph]

I use the mods folder for mods which I do not expect to change when getting online, such as minor effects and new cockpits. Most of what are in the JSGME are mods such as the Zuti_MDS, which you might need to turn on or off quickly and easily in order to be compatible with an online sever or coop.
I use JSGME when I'm getting ready to join a coop or online server, so I can join without issues. Maybe I'm just lucky but JSGME works without a hitch for me most all the time when I need it.