When the Holy Spirit speaks to you there is often an internal struggle. For what He says to you can be at odds with what you currently understand and have been led to believe.
This is normal if not a little disconcerting. Don’t panic, you will find that this will happen a lot. The tension it creates can be exhausting as you try to piece it all together and make sense of it. He understands that and the very fact you are going through this process means you are taking it seriously.
He is not trying to confuse you, rather get you to ask the right questions. He is drawing you into this wonderful relationship with Him and He is daring you to ask those difficult questions. Provoking you to have a different thought.
What you believe is what you believe, so start there. He will take you from there to where you are going. You may have a lot of theology, lots of doctrines, principles and philosophies. At the end Jesus is perfect theology. It is interesting that even much of what Jesus says can be challenging to understand when He uses parables. They can be very cryptic.
There is a reason for that. I suspect one of the reasons is so that you can’t rely on your intellect. It doesn’t mean your brain is redundant.
He has gives you the Holy Spirit who will help you to appreciate what He is saying. He speaks to you right now and as you read the scriptures. Even His disciples had to ask Him to explain what He meant, so you are in good company.
Be comfortable when you don’t know everything all the time. It can be frustrating, I know. The Holy Spirit knows everything and He is a genius. That is why I cannot stress enough the importance of learning to hear Him clearly. Practice training yourself to be led by Him. It may take time to get it right but He is a good and patient teacher. Be kind to yourself in that process.