there are 2 main peripheral documents:
for non-core peripherals: usually APB1 or APB2 (see RM0008 figure 1 or figure 2)
for core peripherals: PPB (see PM0056 table 33)
the peripheral gets its clock from its bus (usually APB1 or APB2)
APB1 and APB2 divide the AHB clock to get their clocks
the AHB clock comes from the SYSCLK which is usually the internal RC oscillator or an external crystal oscillator. this is selected in an RRC register (see RM0008 7.3.1 & 7.3.2 or 8.3.1 & 8.3.2)
most peripheral clocks are disabled by default. they will need to be manually enabled via the RRC registers (see RM0008 7 or 8)
for non-core peripherals: see RM0008 3.3, table 3
for core peripherals: see PM0056 4.1, table 33
RM0008 will usually have a major section for each peripheral with a sub-section for its registers. here are some:
by default, I/O pins are mapped as GPIO. if different functionality is needed, the pins need to be placed in alternate function mode (see RM0008 9.2.1 and 9.2.2)
when a pin is in alternate function mode, its alternate function is determined by its alternate function mapping (see RM0008 9.4.2 and 9.4.7)