よい is an older (and more formal) form – over time, the pronunciation shifted to いい, but it’s still よい at heart (which is why it switches back to よ~ whenever it conjugates – i.e. いい, よくない, よかった, よくなかった et cetera).
Basically, just use いい. 良い is probably going to be read as よい… I think… but noone’s going to bat an eyelid either way. If the reading is particularly important, there’ll be furigana.
Lots of readings have shifted over time – for example, if you ever see a long-o sound represented as ~おお, that’s because the second お used to be a ほ. For example, とおり used to be とほり. All languages have vowel shifts over time. English’s was particularly drastic. =)