Custom fields should be selectable by the PDF design. If you want a custom field to be a part of all PDFs then select all the PDF templates you have created. Example: I have 5 PDF templates for Invoicing customers. I only want the custom field to show on two of the templates, not all 5. by having the custom field show on all PDFs the default information input in the custom field will not be relevant to all PDFs.

Also, allow the selection of the template at the beginning of creation of the Invoice or Quote or whatever, not after it was created.