The Batch Upload and Upload Checks that Paytrace refers to is different from the batches that are run in Salesforce. The Batch Upload that Paytrace refers to is the method of uploading a file to initiate and process electronic checks. AppFrontier sends each one as a separate transaction using API calls. This means there are no file transfers for ACH.
The batch that runs in Salesforce is separate and only running in Salesforce. This is what allows Salesforce to know when to process payments and which records should be sent to Paytrace. It batches the transaction within Salesforce to be processed as individual transactions at the Paytrace level.