Speaking from my own experience, I advice you to consider to integrate the two systems. By doing so, you will create 1 (one) Quality management system (your companies Quality system). You can create a "cross-reference table" to:
a) Check whether all ISO norm elements and BRC clauses were implemented (you can put the numbers of the ISO and BRC chapters in the table)
b) Easily find the concerned procedures or quality documentation in your quality system
For the numbering, you can continue with your current numbering system (if this is working well and if your colleagues are used to it). That avoids you to change the numbering, each time that there is a new version of ISO or BRC.
I hope to have informed you sufficiently.
Afaik, an ISO "Quality Management System" in the Food Industry excludes Safety-related issues. Hence iso-haccp as in iso22000.
IMO, in the specific context of Food Safety it is preferable to equate "Quality" with the, i think, US concept of "wholesomeness".
Unfortunately BRC, probably as a result of Due Diligence requirements, enhance the confusion by including patently non-safety related issues within their renowned "Global Standard Food Safety"
IMO it is preferable to avoid blending two Standards intended for basically different-purposes into the same "Quality Manual" (another paradoxical terminology but whose misuse is so well established as to be unchangeable).
As far as choice of numbering goes, as long as it's internally consistent, Standards IMEX invariably place no specific requirements on such, eg see this thread -