After starting your employment as a PhD student, a research plan is made, including an overview of the courses and workshops that your supervisor recommends you to take. The supervisor is responsible for proper coaching, which includes of course getting the best out of you, and monitoring progress in an informal and formal way. The process of becoming a full-fledged researcher takes time. A useful guide is the booklet written by Patricia Gosling and Bart Noordam, Mastering your PhD.