η, υ, ι together with the combinations ει, οι, υι (if you ever come across the last one, being a rather rare case) are all pronounced /i/ The reason for all this diversity is the etymology (the orign) of the words and the historical development of the greek language. There are a few rules that might help you with the right spelling (ορθογραφία) but mostly it's a question of writing down the word again and again till you get used to the way it should "look". (Same with english. Why do we write "night" for example, when we pronounce /nait/. It's because we get used to it's spelling and not because we get to dive into it's origin, or anything of the kind.) Same with ο and ω. They are both pronounced /o/ You just get to learn, for example, that verbs are always written with an -ω (παίζω, μιλώ etc.) One of the rules I was talking about. Learning Greek can be a pain, but it can be rewarding once you make your breakthrough. Good luck!