Cipulot

First of all.... what are you planing to "create" for PCI_Express?? A comunication card for serial/parallel controll or more complex stuff?
I think that you should first decide the project (a very basic one), look around and search for the easiest one. Second you have to get a Schematic/PCB design software: something like OrCAD Capture and Allegro is a good start, they give also a free (but project size limited) student version. Note that for this you have to get at least a pcb layout prototype for the pci-e card dimensions(for what I recall there aren't in the examples folder). Next learn the basic specifications and requirements for the PCB structure (layest and trace capacity for the power that the project might need from the internal pcie power delivery (I belive is 75W max, without power connectors). Maybe you can find some projects online for free (look on site of electronics, maybe on the EEVBLOG). Once you've started maybe switch to a more "all in one" software solution, like Altium Designer. They have pcie card template with pre compiled specs and are free to download from altium repository website. You can even import OrCAD Capture and Allegro projects into Altium with the incuded tool.
I hope I've helped.