I don't learn specific kanji, rather I learn words containing kanji. That way I don't worry about kun/onyomi. Just make sure you learn vocabulary and when you do, focus on the kanji after you get the meanings down. Hope this helped, good luck
For my exam, i must learn over 100 characters, and i've thought about learning what the kanji are composed from / by logic, but it doesn't always work ^^ ; i don't know what heisig method is, but will check it out