PWM is available on the timer pins. The SAM D series has two different types of timers, "Timer/Counters" and "Timer/Counter for Control Applications". These are labeled TCn and TCCn, where 'n' is the timer number. TCC timers have more features that make them better for controlling power stages (for motors or switching converters) than TC timers, but both can be used for basic PWM. TC timers have two waveform outputs and can do two PWM channels per timer, TCC timers have eight waveform outputs and can do four PWM channels per timer (the extra waveform outputs are usually used to provide complementary PWM outputs, like for controlling an H bridge with separate high and low side drive signals). The waveform outputs are labeled like 'TC5/WO[2]' or 'TCC3/WO[0]', where the first part is the timer and the bracketed number is the waveform output. The two timer types have their own sections in the datasheet that will explain how to use their various features.
SPI is available through the SERCOM peripherals. Rather than having separate SPI, USART, and I2C peripherals, the SAM D series uses one SERCOM peripheral that can do all three of those. This is actually one of my favorite features of this MCU family because it makes the parts very flexible and tends to make PCB layout easier. Each SERCOM has four IO pads, which can be used for different signals in different modes. There is a section in the datasheet for each SERCOM mode, so if you look at the "SERCOM SPI" section it will explain how to use it. Under the SERCOM SPI section, look at the Control A register in the Register Description section. The DIPO and DOPO bit fields control how the SPI signals are assigned to IO pads, and the tables for them will show what signals can be used on which pad. Like with the timers, the SERCOM pin functions are labeled like 'SERCOM4/PAD[2]' where the bracketed number is the pad number.
Since you said you're replicated an Arduino that used a different SAMD21, do you actually need to worry about all of this? Depending on which SAMD21 is used in the Arduino you're replicating the only difference may be the memory size, all of the libraries for SPI, PWM, etc might just work and you can go by the pin assignments the arduino thing offers.