They won't just slip in your current manual in numerical order without a great deal of work. Of course some procedures required under SQF will already be part of ISO 9001 such as managment review, internal audit, document control etc. What I would do is look at what you have in ISO 9001 and then check the requirements of SQF and extend procedures in your current system where possible.
Personally I would have one manual that includes your quality policy, food safety policy and any other policies. Or you may choose to write a combined food safety and quality policy. Then the organisation structure(s), you may well have an additional organisation structure outlining your food safety responsibilities as the structure / personel may be different to the quality structure; it could be the same, depends how you are set up.
In terms of procedures you need to write and implement them to cover SQF requirements, but they can be referenced in the various sections of ISO 9001 e.g. pest control, factory standards, cleaning etc. would surely go in 6.3/6.4. HACCP in 7/7.1. etc.
in my opinion it is desirable to have:
- a top level manual that references procedures
- a HACCP manual
- where possible procedures that cover requirements of both standards
- additional (standard specific) procedures
- then all of your documents, forms, checklists etc.
4.2 Documentation requirements
5 Management responsibility
5.1 Management commitment
5.2 Customer focus
5.3 Quality policy
5.5 Responsibility, authority and communication
5.6 Management review
6 Resource management
6.1 Provision of resources
6.2 Human resources
6.4 Work environment
7 Product realization
7.1 Planning of product realization
7.2 Customer-related processes
7.3 Design and development
7.5 Production and service provision
7.6 Control of monitoring and measuring equipment
8 Measurement, analysis and improvement
8.2 Monitoring and measurement
8.3 Control of nonconforming product
8.4 Analysis of data