Using MySQL Workbench, what is a good way to do development on an alternate server and copy changes to the main server?
What I traditionally do, if I can't sync between databases, is take a copy of the schema, add  dummy data, and develop on that locally. Then I save all my modification scripts and run them on the main server when I'm ready to push. 

I would avoid moving data from development to production. Production -> Development may be fine if you don't have large amounts of data. Otherwise, use a dummy data generator if you can.

Ultimately, you'll have to develop your own methodology just like you do when you introduce version control or backups to a project. It is dependent on the situation.