I have a question. So when I want to update the save file into the new build do I have to take the save from inside the game itself or the folder??

You can just copy all the save files and paste them over the ones in the new build. You need the config.rpgsave and global.rpgsave files too, so it's just easier to delete the save folder from the new build and then paste the save folder from the old build in the www folder.
This post tells you how to do it https://spedumon.itch.io/small-on-top/devlog/1285675/small-on-top-public-build-0...