Yes, there will be evil factions. The clergy of iuz, the palace guard, the city guard, the horned society, the rookroost thieves guild... there will be plenty of factions and opportunities for people who wish to play evil characters and have faction support, aligned with Iuz or not.
As for the Seekers, I assume you mean the Seekers of the Arcane. I have no problem with members of such an organization being on the server, but I don't think I'm familiar enough with the group to know whether or not they'd have a base of operations in rookroost or the surrounding areas. Post any information you have on the group here and we can look at how they'll fit into the setting.