Your situation is by no means uncommon. In fact the vast majority of students starting JAR ATPL(A) modular couses have learned virtually nothing from their PPL theoretical knowledge studies. This just makes it more difficult for them to get to grips with the ATPL material.
The good news is the fact that you appear to have recognised your error. Now providing you do your best to learn and understand as much as you can from your ATPL course, no permanent damage will have been done.
Unfortunately a small proportion of students carry the "just learn the answers" approach on to their ATPL studies. In most cases this does not prevent them from passing the exams, but they gain nothing more from the process.
You should try to learn and understand as much as you can from your ATPL course. Some of the material is over the top, but much of it will be useful in developing a wider understanding of your chosen career.
Past students sometimes ring to tell me about their interviews and type rating courses. They often comment on how much of the apparently irelevant material from their course proved to be very relevant. Curiously enough I have never had such a call from the small group who have concentrated on learning only the answers to the exam questions.