mysql replication and innodb_file_per_table
Yes you can use innodb_file_per_table = 1 for your slaves.
Additionally take below points in your consideration

If you have same version on MySQL on both Master and Slave. You can directly take backup and setup replication from Master to Slave by adding  innodb_file_per_table = 1 on slave in my.cnf
Please have a look at How to set Master Slave replication

If you have different version of MySQL , Please make sure that you are taking backup properly because different version would have mismatches in System tables (MySQL Database).
Please have a look answer by @RolandoMySQLDBA for How to take backup properly