Whatever OS/applications you have run in low priority ISR contexts, taking however much time they wish. When a high priority interrupt happens, the lower priority ISR contexts are preempted and then resumed after the high priority ISR is complete. Go have a look at the design and the SRP model behind it; your questions are directly addressed there.
Comments
How would it handle kernel/user space if everything runs inside ISR context ?
Whatever OS/applications you have run in low priority ISR contexts, taking however much time they wish. When a high priority interrupt happens, the lower priority ISR contexts are preempted and then resumed after the high priority ISR is complete. Go have a look at the design and the SRP model behind it; your questions are directly addressed there.