Inside-out Project

I just finished a project on Japanese grammar and how it subordinates complex ideas. Backing up, let me explain better: In a language, the first thing you learn is the order of the sentence the patterns of very simple sentences, but to really communicate showing how one idea effects another, we use "if" and "when" and relative pronouns like "that," "which," "who" and many many more. It's the way two ideas like "Jacob ate a pie." and "The steak was made of mud" can become one sentence: "Jacob ate the pie that was made of mud."Now, from that first day of Japanese, I knew that this was a language opposite to mine in order, but not until I practiced the sentence patterns of subordinate clauses did I realize that speaking another language can also be inside out. I compared it to an orgiami figure--inwardly often very complex but with a little study and a gentle pulling apart analysis, the thing becomes understandable and best of all, reproducible. I'm still pondering how I can make these patterns my own. How does a language form like this become second nature? I find I do a lot of drilling and reading and writing and translating my more complex thought in written words rather than the spoken bursts and phrases which too often make up our speech, I've improved a great deal. I also find that it's been one of the first things to deteriorate as my own language pattern becomes the norm. For some reason, I retain the vocabulary so much better. I'd love to hear any thoughts that might come from others who have thought about this.