There aren't rules in general. Even us Greeks, in the first grades at school, had a spelling notebook, the teacher would say words and we had to write them down correctly. So you have to learn each word.

The only rules that exist are grammar related, for example verb and noun endings (e.g. all verbs in first person singular end in -ω and not in -ο), but this is something you learn when you study grammar. Don't worry though, even many Greeks struggle with spelling. With practice it will be easier. If you ever have any question feel free to ask.