If I have a XOSC32 oscillator on PA08 and PA09 pines , then it is possible for me to use it for all my modules?
It is possible, but you really should not do this. You will slow down your whole system to 32 kHz. That's like 100x slower than first processors
But do I keep them clean clocks to each module such RTC_GCLK_ID?
I don't understand what do you mean here.
It goes like this. Each and all peripherals can use any of the GCLK[n] generators. So total number of frequencies used in the system is limited to number of GCLKs. But the most complex system I've seen used only 3, so you have plenty.
Each GCLK[n] can have one of many clock sources as an input.
A system configuration may look like this, for example:
1. Internal RC [8 Mhz] -> GCLK[0] -> all peripherals that need to run fast.
2. Xosc32 -> GCLK[1] -> RTC for accurate time-keeping.
3. Internal RC [8 Mhz] / divided by 3 -> GCLK[2] -> some weird peripheral that needs 2.666 MHz clock.