Easy.
- Add the game's version to the zip filename (you can optionally also add it to the game filename or even in the game itself, for ex. in the game's main menu)
- Make a post each time you make an update which include the new version and what changes/fixes that version contains. You can use the itch.io devlog posts for these posts to avoid putting everything in the game's main description.
Itch.io itself ask you if you want to make a new devlog when you upload a new file.
- Add a text file in the zip files that contains a text listing of all the versions & their changes/fixes.
There are plenty of example on itch.io alone but if you want an example of the first 2 points check a previous game of mine
https://negator2vc.itch.io/the-lost-galleon
https://negator2vc.itch.io/the-lost-galleon/devlog/221551/version-21-released
Also it's best to keep the previous version up, at least for a couple of weeks, in case the new version introduce bugs.