There are tradeoffs for almost any choice that you are going to make. If you are looking for a list of dos and donts, you are looking for the wrong thing. No one will be able to give you a handy list of things to do. What you do and don't do depends on the needs and design of your application.
If you are extremely new to MYSql, you will have to learn how to use explain plan to optimize queries.
This is a good place to start. It tells you how to ue explain plan, and optimize your sql queries. Don't worry about optimizing the database settings for now. Mysql comes with inbuilt .cnf files based on the size of the database. Just use the one that matches your requirement closest