They're completely separate entities. They share the same goals, safe workplaces, workers rights etc, and often work together, but the ETU represents sparkies, the cfmeu is the largest union because they represent plasterers, chippies etc etc
Whoever best represents their members interests at the time. No different to any other person voting for what suits them best.
Last election I'm pretty sure they didn't give us any voting advice other than informing us of Tony Abbott's intention to rape us