When using the batch regular payments to process your regular payments, you can specify the payment method that these will be allocated against.
If this is not set they will be allocated to the first payment method you have alphabetically
To set the payment method for regular batch payments go to Setup > Generic Parameters > Regular Giving Settings
In the settings for Set All Payments Made as Payment Method of select the payment method you wish to use for the batches. Scroll down and click Save Changes
This will apply to the next batch – all payments will be coded with that payment method selected. You can create further payment methods at Setup > Payments > Payment Methods