There are three types of batches that can be enabled and set. They should be set to run daily in order to pickup and process all records that apply.
Transaction Status Batch: This will sync up your ACH transactions providing you have one of the gateways that have this feature available.
Payment Batch: This will allow you to process recurring payments based off our Recurring Payments option.
Finally if you have Payment Requests enabled (Site's and Platform Edition) you can also setup the Account Updater feature. Account updater will check for credit cards that will be expiring in the next 30 days and send an email for the customer to update their credit card information.