Cyclone V EMAC to FPGA Setup

Hi, I'm new to hardware/embedded level development. I've picked up a Terasic DE1-SoC Cyclone V board to start working with. I've gotten through quite a bit of basic FPGA work in Verilog with the board. I'm trying to move on to interfacing with the HPS peripherals. I've found a few tutorials, but unfortunately every one of them starts with a "Use these pre generated files/etc" to get started. I'm looking for some introduction level learning that covers what happened in that pre-generated land to actually understand how to start a new project of this type.

I was hoping to get the EMAC interfaced to the FPGA in a project. I kind of got something going using a few tutorials, but I don't feel like I got it quite right. I was wondering if someone could give a bit of an example walkthrough from new project in Quartus/SystemBuilder/Qsys through something simple like getting a PHY carrier sense to an LED.

I've been using http://www.altera.com/literature/an/an706.pdf as a reference, but I'm really wanting to understand what they have done already for me in the pre-generated steps. There's also quite a few bits like the TCL file which are opaque in what they're doing.

I realize this is a very large request in scope, so thanks in advance for any reference material or advice offered.