There are a number of MySQL client but so far phpmyadmin is one of the popular MySQL client used. It's simple to use, effective and provide almost all the required features for day to day development.
As you know regular backups of DB for a running site are very important. Most of the hosting providers do this for you, but sometimes its also expected from you to do the same.
In the very initial days of my work in Node JS if faced this issue. Though Sequelize provide a great ORM for MySQL but the association within the models is a bit tricky.