So the solution for me was to write a PHP program to iterate through each db's sql file and do the following:
/*
$mysqldir being where the mysql exe is installed too.
$db being the database name
$file being where the sql file is
*/
$exec_str = "\"".$mysqldir."mysql\" -h localhost -u {username} -p{password} -e \"CREATE DATABASE IF NOT EXISTS `".$db."`\"";
system($exec_str, $status);
$exec_str = "\"".$mysqldir."mysql\" -h localhost -u {username} -p{password} ".$db." < \"".$file."\"";
system($exec_str, $status);
Basically: (Partially what @Drew answered with)
CREATE DATABASE IF NOT EXISTS `database_name`
`database_name` < "C:\file\file2\db.sql"
from the mysql command line.