The great man is one who can put into words the will of his age,

Niccoló Machiavelli appears in canon (although he sadly does not have enough appearances yet to be appable) as a student at the same university Cesare is attending (and he did actually go there during those years, although probably not in the role the manga gives him, haha) and was sent as a diplomat to Cesare's military campaigns in the early 1500's. Cesare had a great influence on the development of his thoughts on political theory and science and he praised him in The Prince, the text for which he is now (in)famous. Machiavelli is shown to be already watching him with interest in canon and Cesare already displays signs of becoming that brilliant if idealized leader.

( it's all about power then / take control / breaking the rule / breaking the soul )

In the manga Cesare holds some very strong opinions about religion and God. It was very close to being a deal-breaker for me when I first read it, actually. The first time it came up, I had to stop for the night and go bitch at people about it, haha. But the more I thought about it the more I realized that I could roll with it. This is an explanation for some of what I originally saw to be ahistoricalities, or just statements that I couldn't originally relate to his later life and what people said about him both as an adult and as a student at Pisa.

( I've heard there was a secret chord / that David played, and it pleased the Lord )

So in short, when Cesare talks about God, he's speaking of a singular deity who is involved in the human plane but who is universal in nature. Cesare's God has a will and a desire (and although it's never explained in the manga, I suspect it more or less lines up with the Jewish philosopher Maimonodes' statements on the subject--that humans by dint of being human cannot ever fully be one with or comprehend God although they can move closer to him by aligning their wills with his and trying to more fully realize their potential) and cares more about the big picture (are you a virtuous person) than the little details (how do you worship).

ed I'm going to amend this somewhat to say that Cesare really likes talking about Things. But a lot of the time when he talks about Things he uses other people's ideas instead of explaining his own. He'll quote famous people more often than he will tell you what he actually believes. Also, as he stated in a recent scanlation update, he really does think that God is to an extent in everyone (or that everyone, being made in God's image contains some of that divinity) but that does not mean that everyone shares equally in God's love. ...I think he's really getting more at the social construct of God here, though.