PCIe: Who's in charge here?
Yes, it is the motherboard processor is the main controller. Specifically the CPU or the "North Bridge" is the master of the PCIe bus. This is the same as PCI. However a PCIe device can access memory, but it needs to first request the bus from the PCIe master.
Some PCIe chips can do DMA where they handle transfers by themselves. This is common for network cards. However there is overhead, so it will provide more throughput with larger transfers.


EDIT: PCIe tops out at 5 Gb/s/lane for PCIe Rev 3. It tops out at 16 lanes. That's a total of 80 Gb/s for a single card. That's nowhere near 1 Tb/s, let alone > 1 TB/s. Your goal is going to be difficult. But then I don't think you would want to use PCIe for a > 1 TB/s Ethernet switch. That's > 800 10 gigabit Ethernet ports.