>>238
Interesting how you ask this while using Genki, this is usually a problem for the Heisig users. How do you even meet standalone kanji while using Genki?
Both readings are used.
For example 風呂 (furo) uses the on readings for its kanji.
I don't think you need to learn the readings. If you see some kanji and don't know the word they stand for, you won't be able to guess the pronounciation anyway (because there are multiple choices).
I think the best way to go is by relating the kanji to words (eg when you learn the word, learn how to write it). Genki does just this, so you should be fine. You will pick up the readings as you use them to form the words.