epsilon vs. eta and omicron vs. omega

Dear all,

I’ve just started learning Greek with J William Smith’s “First Greek Course” and I have a major struggle to understand the logic (if there is any) behind when to use epsilon or when eta and when omicron or omega in the middle of a word.
E.g. is there any deductive way to learn that hora has an omega and not omicron? Or that Athena is with eta and not epsilon? The pronunciation wouldn’t help me either, since I can’t know beforehand if the “e” in the word should be long or short.
Or do I just have to learn it as it is and that’s it?
Sorry if the topic has arisen before…

Thanks to all
Matthew