If Enable Chaining is ON, the Individual Batch Limit field becomes active automatically.
You can then specify how many records should be processed per batch during the batch migration. 
PS: View Drag, Drop & Upload Files to Amazon S3, a Salesforce AppExchange app for moving files from Salesforce to Amazon S3: https://appexchange.salesforce.com/appxListingDetail?listingId=a0N3000000B5ZPqEAN