In a standard dual-break setup, physics says put your drogue in the fin can and your main in the payload just below the nose cone. If the main is in the lower section, nearly the entire weight of the rocket (fins + motor case + rings + airframe) are pulling on the junction where the main deploys during the ride down; if the main is in the upper section, it's just the nose cone staying put.
Granted, it's possible with some massive shear pins (and ensuing massive deployment charges). But for the sake of simplicity and reliability, I have almost always seen it the traditional way.