According to Eliot, the organization's main base on this side should be in the City of the Clans since, from there, they can control much of the Kingdom and the Academy itself. If Eliot is a bit conspiranoid, he may think that the Academic Clans that rule the City of Clans, have been corrupted by that organization.
But this is already complemented by what Matthew knows about it. Those guys who were leading the branch of the organization from the City of Clans couldn't get there just because. Clan City is supposed to be one of the safest cities in the world; even though they were in the weakest part of the city, they were still there.
They moved day and night, planning everything from there, under the noses of the powerful, but none of them suffered any real repercussions. That just goes to show that they had a protector.
But going deep into the City of Clans is anything but easy, which is why Matt that time had to retreat.