Hello Tim,
The invoices, estimates and credit memos are children of the Transaction table. For print templates, you can stay with the child tables because they have the unique fields for the transaction.
To set the default template for each transaction, click the More actions... button and select Customize Print Templates... on any transaction screen. In the pop-up screen, you will see dropdowns beside names of the transactions. Select the dropdown you want to set the default template for and choose the template. (Your report must have the same table as its master table to be in the dropdown). Then it's easy as clicking Save & Close. Blank dropdowns mean it is using Method's default report.
Greg