PCIe transactions between two FPGAs through switch.

You’re much too vague in what you need and expect from us. If you start from the PCIe MegaWizard configuration, you will have to write your own PCIe TLPs. There is nothing wrong with doing so, but it requires deep knowledge of PCI and PCIe, and I’d suggest to get hold of the respective official specifications. You will learn about PCI device enumeration, addressing modes, when and how to issue DMA transfers, the magic behind completions you receive and those you send, correctly terminating invalid or unexpected requests, handling interrupts the way you want, and last but not least, writing a correct driver for it.