Brian, you need one management system covering the whole business. One set of documents...this is totally separate from certification. They just come and look to see if you comply with the requirements for the type and scope of the audit you are going for.
Having BRC audit and certify one part of the business operation and SQF the other would be a waste of time, effort and money. It can be done, but you would end up with two certificates one for warehousing and one for production and packing. Neither certificate would cover the full scope of the business activities. Unless there are some ridiculous customer demands going on it doesn't make any sense at all.