This is so funny. Yesterday, someone asked how to do the opposite and I answered that question : Migrate from innodb_file_per_table to off in MySQL
Here the steps for what you want
STEP #1
Set innodb_file_per_table to 0 in my.ini
[mysqld]
innodb_file_per_table = 1
STEP #2
Login in Command Prompt in Administrator mode and run
C:\> net stop mysql
C:\> net start mysql
STEP #3
Convert every InnoDB table to InnoDB again
set MYSQLUSER=root
set MYSQLPASS=rootpass
mysql -u%MYSQLUSER% -p%MYSQLPASS% -ANe"SELECT CONCAT('ALTER TABLE ', table_schema, '.', table_name, ' ENGINE=InnoDB;') FROM information_schema.tables WHERE engine='InnoDB';" > C:\ConvertInnoDBToInnoDB.sql
notepad C:\ConvertInnoDBToInnoDB.sql
Once you view the script and are satisfied, login to mysql and run this
mysql> source C:\ConvertInnoDBToInnoDB.sql
Give it a Try !!!