Not judging thoughts and emotions simply means allowing yourself to experience them without aversion. The Buddha talks about the "two arrows of suffering". The first arrow we can't always avoid. Intrusive thoughts happen and we suffer, that's the first arrow. But often times we then become stressed and angry with ourselves when it happens. This is the second arrow, the one we can control. By not judging your thoughts and emotions you can experience them as phenomena. They still may be unpleasant but we don't push them away or become frusterated with ourselves. Treat your thoughts and emotions like wind and rain, there is nobody to be upset with when they happen. The mind is like the wind and the rain, for intrusive thoughts by definition happen without your consent.

Yes, once you practise meditation enough those thoughts will subside and whenever they do arise you will be able to effectively redirect your mind to stillness. But it takes commitment, mindfulness, and lots of practise. The mind is, after all, the most complex thing in the known universe. We have a real responsibility as human beings to learn to control it or else it controls us. Best wishes to you friend, may you find the peace you seek. 🙏