Developing my own board: Where do I begin?

It's really an iterative process. You'll need to move back and forth between the your schematic / PCB / and Quartus continually through the process.

Here is a rough overview of what I usually do.

1 - Start with determing which IO banks you're going to place specific interfaces on.

2 - I then move to the schematic. Doing the schematic helps you to get a better picture of what the signals are that you'll need. It's helpful to create your FPGA schematic symbol such that the pin names are descriptive enough that you know what they can/should be used for.

3 - Once you've roughly assigned your pins in the schematic, Move into Quartus. Now you can start tweaking your pin assignments and changing the schematic to fit the design requirements.

4 - It's a good idea to envision the physical locations of things on the PCB as you do this. Once you start the actual PCB, you may end up moving A LOT of things around to accommodate the layout. No problem, just change it on the schematic and check with Quartus and the literature to make sure it's a legal assignement.

5 - Whatever schematic/layout tool you use, find the easiest way you can to generate a listing of which signals are connected to which pins on the FPGA. Then use this list to create your pin assignments TCL script for Quartus.

Good Luck,

Jake