USB, UART, SPI difference and usage?
Those are three different types of serial interfaces. 

SPI has a master clock and synchronous master-in-slave-out and master-out-slave-in data: a total of 3 wires plus ground/power and optional chip-select. Data is transferred simultaneously in and out, typically 8 bits at a time. Data can be MSB-first or LSB-first, depending on the connected SPI slave device. SPI is a somewhat loosely defined standard, originally came from the Motorola 68HC11 microcontroller I think. Effectively it's like a shift register.

UART is the peripheral that sends and received asynchronous serial. This protocol is often also called "RS-232(C)" or "EIA-232" or "TIA-232" or "COM port", or several other aliases. This is one of the oldest commonly used serial interface protocols, which is why it has so many names. Unlike SPI, RS232 UART uses a single wire to transmit both the clock and data. As such it depends on prearranged agreement between transmitter and receiver, as to the baud rate timing, the number of data bits, whether or not there will be a parity bit, and the minimum number of stop bits. Transmittting RS232 is straightforward, but receiving RS232 is tricky because of the need to recover the clock signal timing. This is best done in hardware. 

USB is a more modern interface standard that is described in detail by the USB Implementors Forum documentation; I won't rehash the standard here. USB uses differential NRZ signalling and is thus much more complicated to describe at the wire level. Typically you use USB by adding handler code to a hardware USB Serial Interface Engine embedded within the microcontroller, or else use a PHY (physical interface) chip. You can't really bit-bang USB in software, as you could with RS232 or SPI.

You didn't ask about Ethernet, that's yet another serial interface and yet another complicated but well-documented protocol.

The important thing is that "serial" by itself is just a word, not a complete standard.

If you haven't already, you should grab the datasheets for your Intel D1000 MCU and start skimming the table of contents. There you will find sections that describe in great detail, exactly how each of the MCU's peripherals work.