Well, usually things do start to make less sense the deeper you get into it. At least, that’s how it starts. I thought I knew everything there was to know of organic chemistry because we had touched on it in my general chemistry class. I quickly found out after signing up for organic chemistry that I really knew nothing, so nothing made sense. This is why we keep learning everything we can, so that it will eventually make sense.
The Bible came as a shock to myself as well. I heard from it and of it a lot in my childhood, but I had never gotten very far in reading it on my own. I may have read the first chapter of Genesis my first go at it (I was in high school at the time). I quickly gave up on it until I got into college, and read it all the way through within a year and a half after starting it the second time. I mostly heard from the Old Testament as a child, so I was already somewhat familiar with it when I began, but I understand that it’s hard to take everything in it in a literalistic way.
That’s why we shouldn’t take things literalistically. The Bible is a library, not one single book (even though we can fashion all of its individual parts into one volume). It contains some very literal and historical facts, as well as allegory, and certainly everything in between. Jesus Himself frequently employed hyperbole, and then there were times when what He meant was precisely what He said. Just the same with everything else in the Bible’s pages.
Using Catholic Answers is a good start- this is where I started, and it’s been indispensable. You should make use of both the forums and the “main” site. You should also find a good study Bible. The Ignatius Bible is the best one that I know of, but unfortunately only the New Testament is completed (you can buy some individual books from the Old Testament, but that’s going to be costly).
You should also talk to actual Christians. Ask them (us) what they (we) think. For Christians of the Catholic variety, we also have Church history and our magisterium to point to for guidance, so our theological tradition is very impressive. We’ve probably answered, or are answering, any question you could possibly imagine- that may just involve you taking some of the answers to individual questions and fashioning them together to find a more precise one.
I hope that helps.