Lyric discussion by nerdyguy 

Cover art for Entangled lyrics by Honest Bob and the Factory-to-Incentive Dealers

It sounds as though he's comparing a relationship to quantum entanglement (hence the name of the song). In QE particles that were once close, and then separated can still reflect changes made. Simply put, if one changes the other "knows" it. This explains the binary nature of many of the lyrics, what affects one will effect the other. It's elegant and nerdy, I expect nothing less from the geekiest band I've ever heard.