I'd use SQLCMD and run a .SQL file against multiple databases/instances.

I like out of SQL Server processes for this, because I want to deploy easily, or push out, without being depending on a db being on an instance. I have moved them before for load/consolidation issues, and I like flexibility.

SQLCMD -s instance -d database -i mysql.sql

Use a loop or parameters, or even just Excel to build a series of these for the files you need to deploy.