So, as the title says, is there any way to manage which files I wanna download? The problem is that I made a new game of Witcher 3 few months ago, and deleted all the old saves, but everytime I sinc the local files with the cloud, it downloads every file, even chekpoint ones, so I end with 30 or 40 games that I don't want.

So, is there some way to just upload games and not downloading them too?

Not really.
The cloud save mechanism fires up when you start the game and when the game's process no longer finishes. It compares the local version with the cloud one, and downloads what's missing before the game starts while uploading what's new when the game ends. It will also delete from the cloud any file that's no longer there, so this can be used to remove unwanted saves, but that may not be what you want.

So, start by downloading a copy of your cloud saves to have as a backup. Start the game, then while the game is running delete your current saves. When you exit your game, the cloud saves should be removed as well. As I said, not exactly what you're asking for.