What do I want to know/learn about writing?

First of all, I would like to learn how to organize my thoughts in a way that they make sense. I usually write the same way I would say it. By this, I mean I literally write exactly how I would phrase something. I think I have the habit of doing this because I want the reader to feel as if I where telling him/her my thoughts. I use many examples in my writing to get my point across,but I don't know if that is acceptable in writing? I would definitely like to know what is a, "well written paper." In regards to this I am not talking about grammar, but more like content,thought and idea. I have a bad habit using fragments and run-ons. I don't know where to stop! I definitely look forward to minimizing or better yet eliminating that habit from my writing.