If I already bought the game on itch ,do I have to pay for the update?
No, if you've bought the game here you get all future updates for free
How?
Your library.
I had this same issue when I first joined itch.
For some stupid reason the site isn't coded to register your purchase on the game pages. So you need to go to your library and it'll be in the top row with the rest of your purchases.
