How did Jonathon Gilbert write in his journal about Stefan killing him? I mean, he was dead, right?

I thought the same , but he had that ring , the one that Jeremy has now and he survived. :)

He survived Stefan's attack. He died later.

i thought so too but then later on stafan said he didnt know he was going to survive

You can survive an attack with the ring, you cannot die with the ring on. Stefan tried to kill him,later wrote in his journals re watch the episode.