If you don't know basic PHP then you're going to be in for a whole world of hurt! BUT... it's just a learning process, so don't get too discouraged yet. :)
Some links that may help:
http://php.net/manual/en/introduction.php
http://www.codecademy.com/courses/web-beginner-en-StaFQ/0/1?curriculum_id=5124ef4c78d510dd89003eb8
As far as what functions to use where... that's determined 100% by what the plugin needs to do. There's no one thing that can tell you what to do because your plugin will be different to everyone elses.