Seeing most of them are Visual Novel, what program do they use to make that?
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. That, I can't help with because I don't use it.
Ren'py comes with a tutorial that goes over all of the basics when you download the latest version. You don't have to know all of the ins and outs to get started as several aspects can be added as you code (Images, transitions, font, etc.). The system is based in Python and will essentially teach you how to code if you let it. "If" statements, call backs, variables, and more are all covered in the tutorial, and if you have any errors that pop up as you play-test your code, or don't know how to code something specific, there are many coding resources online at your disposal. A quick google search will usually do the trick and take you to the Ren'py website, stack overflow, or a number of other forums where game creators have discussed their challenges.
The beautiful thing about the community is you can ask just about anything and some talented coder has probably done it before, and is willing to share.