How can I determine the check advanced pdf layout that is used on Bill Payment, Check, Cash Refund and Customer Refund? For Bill Payment, Check and Cash Refund, is it the PDF template on the transaction form? If so, how about for Customer Refund that does not have the PDF template field in the transaction form?

On the original form (Sales order, Vendor Bill etc) there is a tab for “Linked forms” there you can specify a related form (Cash Sale, invoice etc). That linked form can have a custom PDF assigned to it.