* How do I do board layout?
You learn an EDA tool such as Eagle, pick a board vendor, and produce a design that meets the board vendor's specifications. You submit an order, and get boards in the mail. It's like designing and getting custom t-shirts made, expect much more involved.
* How do I know which components to put on a board?
Mostly datasheets. Once you identify your subsystems (I want this micro, that USB interface, this video chip) you get the datasheets and read them to learn how to design the schematic for that part. How do you pick what micro or USB chip? I start by browsing hobbyist websites to see what is popular and digikey to see what meets my specs and is cheap.
* How do I know what components go where?
On a hobbyist board running in the kHz range? They mostly go where they fit. There are no rules, just guidelines- group things by how they connect, so you have less wire everywhere. Rats-nests are hard to design and debug, and component placement is the #1 way to fight rats-nest. Put central components (like the microcontroller) in the center. Put ports on the edge of the board. Put the USB chip next to the USB port.
* How do I test the system I want to build.
You build it. There's no simulation. You build it, and if things are wrong you figure out why with a multimeter and maybe an oscilloscope.