Hello Goran,
from my point of view, PIT is much more better than STM. PIT timer counts down from set value (LDVAL register) to 0. After zero is reached Timer Interrupt Flag is set and timer counter (CVAL register) is reset to original set value (in LDVAL register) and process is repeated. This is pretty simple and it perfectly fits for your task.
STM works different. There is compare register you set and timer counts from 0 to FFFFFFFF. After compare register is reached, Timer Interrupt Flag is set, but timer continue with counting up. So in every interrupt, you have to stop counter and reset it's CNT register to 0 and enable counter again. In this case, timing is not as accurate as in case of PIT timer.
Hope it helps.
Regards,
Martin