Thank you everyone for your advice, links and experiences all of which will add to my (slowly growing) knowledge.
For clarity my FTO and instructors did in fact cover everything (like using the mixture etc) however as others mentioned, some subjects are more relevant to the airfield you are learning at - mountain wave hardly ever affected the airfield and it was never experienced in flight so it was never discussed in any detail. Having said that I now wonder if the topic should be covered better.
SNS3Guppy - couple of great posts on the subject so thank you for your time and effort explaining and in particular the 'what to do if...'!