Have the foundation ditch uniforms, opting instead to adopt the uniform of the relevant local authority. Using somewhat fabricated documents to get access to whatever they need, using powerful people in the loop for leverage and authority. You would obviously need a formidable hacking team to erase any trails left by botched operations, though I imagine most physical clean up can be left to authorities. Any damage can be framed as terrorists, and if that wouldn't work for some reason, Wormwood would probably have a specialized clean up force, though they are rarely forced to do any ground work.
Most agents would be recruited locally, giving them connections to powerful agents of other organizations. Wormwood would likely use sleeper agents planted in the CIA, FBI, Interpol, and whatnot. This way even if an agent is entirely found out, it could be pinned on the CIA. They would all have some kind of remote detonation system, allowing them to be executed should they be caught. In case of an agents detainment, the hacking team might plant traces of the agents connection to terrorist organization to excuse the poison capsule or whatever.
Any group of this size requires some kind of base of operations. I think some phony tech shop would suffice, as any gear would blend in with the stock of the shop, and the base doesn't need to be big. Of course they would likely have a black site for training, but other than that they just need a place from which they can transmit orders to their agents.
If they need an armory for some high tech gadgetry, it can be stored in the basement of these shops, and shipped remotely using local government trade routes. I imagine they don't so much invent new tech in house, but rather take the top secret weapons from governments in the loop.
If you want to take a more "hiding in plain sight" approach, they could have a public face as the Wormwood foundation for the homeless or something. Framed as a non-profit that does occasional work to hit the headlines, their branch offices are probably empty though. Housing any important info in a public facility would be stupid, so they might take the radio shack approach for their important stuff.
There would also be an inner ring of agents recruited from birth. Orphans or children of agents, these would be the team responsible for all the management. Each agent is assigned to monitor major figures who are in the loop, though obviously they don't watch everyone. These agents aren't responsible for any ground work, instead taking the role of monitoring, management, and safeguarding. But obviously there can still be the super spy raised from birth if that's the angle you're taking. These agents are isolated from the outside world, and if you want they can be developmentally stunted and incredibly creepy.
Last thought, for the remote detonation system, the agents could have metal plates in their heads to excuse metal detectors going wack. Sorry this is so long.