I use codesmith to generate scripts for new tables but other than that I write upgrade scripts by hand if I need to alter a table. There is a codesmith template that you can point at an MS SQL table and generate the table script for MySql. I "think" with newer versions of Codesmith there might be a driver where you could point at MySql tables for script generation, but you would probably need to make custom versions of codesmith templates since mine were built and tested only against MS SQL and based on MS SQL data types.
If you have some other tools for working with MySql and generating table scripts, you can use whatever works.
Hope it helps,