There are actually two questions here: 1) how to create protocols, and 2) how to test a PCB. In general, protocols are generally for design verification and validation or process validation. There is a GHTF guidance that provides a great template for protocols to do process validation: http://www.imdrf.org/docs/ghtf/final/sg3/technical-docs/ghtf-sg3-n99-10-2004-qms-process-guidance-04010.pdf
In addition, your blank template should always include the following elements:
1. purpose
2. scope – especially what is not in the scope
3. references to standards that are applicable
4. revision history
5. list of equipment – including calibration ID
6. possibly a reference to detailed work instructions for methods (if not in the protocol)
7. description of samples being tested
8. statistical rationale of sample size
9. justification for choice of samples (worst-case scenario for each test)
10. acceptance criteria
11. review and approval of the protocol
When you write your test report, auditors always look for deviations, and a conclusion stating if the acceptance criteria were met.

Regarding PCBs…there is a J-standard for inspection, there is inspector certification to that standard, there is certification of trainers for that standard, there is validation of the process (e.g., solder masking and wetting of components with solder), there is automated optical inspection, ICT fixtures, functional test fixtures and x-ray inspection. The design and complexity of the board often determines if some or all of these methods are appropriate.

Thank you Robert for the detailed answer. It gives a good guidance on developing protocols.

You’re very welcome:)