How Do I Reflect Upon and Connect With Different Ideas in a Book?

In the beginning it's totally fine to just imitate the author's thinking as you say. In NLP they call it modeling where you are imitating someone better than you. I actually recommend that you do this like with public speaking, giving presentations. Then you start to get a big variety of experiences and influences and then you combine them to create your own style,. But that takes some time. That's kind of happens at the advanced levels.