The FIPAs tend to provide investor protections. What they are is an insurance policy to ensure that the investor is treated fairly, and also as if they were an investor of the domestic country. So they tend not to have permanent secretariats on these agreements, because it's a framework within which your investor can bring a claim against another country if they're not treated in accordance with the agreement.
Now, most of these disputes are settled in the context of organizations like ICSID in Washington, which is a World Bank forum. There is a small secretariat there, and it's paid for by the fees that are levied against the parties to the disputes.