Here are some things I do that I find helpful for philosophical and theological things (like you, I don't do things for academics, I do it for my own sake):
1) SQ3R is helpful. You want to start by getting the lay-of-the-land. It can be helpful to read Wikipedia articles or get an edition of the work that contains a summary. As an example that isn't quite philosophy, I found the "Landmark Herodotus" edition of Herodotus pretty accessible, simply because it contains some essays that give color to how to read it. If the thing you are reading doesn't have such an edition or a decent Wikipedia article, just skim it quickly to get a sense of what it's all about.
After scanning, come up with questions you'd like to answer after having read the text. You must have some reason for picking this text as opposed to another - why? What are you trying to get out of it?
2) Keep a notebook. As you come across an interesting passage, either write a page or two about why it's interesting to you, what it reminds you of, what questions it answers, etc., or mark the passage and come back to do the writing later. Writing something down forces you to think it through more thoroughly than simply stating it in your head.
3) Go back through your note book periodically. As you progress through a work (or read other works), you'll see different things, be able to expound on earlier ideas, come up with further questions, etc.