As for the slmod mission folder - I understand that Windows 7 has folder aliases(?) - but I have never used them. Perhaps the slmod mission folder can be an alias of the DCS..Missions folder so that the mission files do not need to be maintained in two places. If anyone knows how/if this works let use know?
The slmod missions folder is where the mod will look for mission files if you want to change the mission via slmod admin commands.