Point me in the right Direction - PCIe

The PCI spec probably makes slightly easier bedtime reading! Once you'e loosely understood a bit about how the bus works (logically that is), you can then think a bit about PCIe. PCIe is basically PCI using hdlc frames instead of a parallel bus.

The Altera PCIe slave isn't fast - when fed through PCIe->Avalon interface single cycles are positively lethargic (think ISA bus speeds, then slow it down some). Fortunately a PCIe transfer can carry a lot of bytes (probably 128) and the per-byte cost is small. Unfortunately you (almost always) need to start with a DMA engine in order to do multi-word cycles.