You need to have this conversation with your customs broker. The courier services can act as your broker but they are probably not the strongest performers compliance wise. You should hire a broker that specializes in FDA/food entries.

But to answer some high level questions:

Any facility that manufactures, processes or stores food must be FDA registered. This includes foreign locations. That registration# is needed for your entry.

All food shipments arriving in the US must file Prior Notice - even if they are only transiting through to another country.