The container types don't have any relevance to the USPS package rates our system looks up; we might just as well have called them "Container A", "Container B", etc., but we figured naming them after a range of actual container types and sizes would be easier for sellers to keep track of in their configurations. E.g., if you don't ever ship in actual envelopes but have more than 3 different types of box, you could use our Sm/Reg/Lg Envelope container types to define actual boxes and just remember that our Sm Envelope "really means" a certain type of box for your own reference.
Products configured to ship in the same container type will consolidate into common containers according to packing capacity. E.g. if you have Product A configured to ship up to 2 units in a Reg Box and Product B that ships up to 4 units in a Reg Box, then an order for 1 unit of A and 5 units of B would add the cost+weight of only 2 Reg Boxes, since the "empty spot" in A's box can be taken by 1 unit of B, and the remaining 4 units of B can fit in a single Reg Box as specified in B's settings. Tube container types can also consolidate from smaller into larger Tubes, so in the example above if we'd said A could ship in a Lg Tube and B could ship in a Sm Tube (all other units/capacities being the same as above), then the example order would add the cost+weight of only one Lg Tube and one Sm Tube to the order.
If you wish to use our standard USPS.com rate lookups, just define each container type you're using with its (empty) weight in oz., configure each product with the weight of each unit in oz. and specify how many units of that product will fit in what container type. Any shipment weight totaling 13 oz. or greater will always return the Priority per-oz. rate (since First Class is only available up to 13 oz.).
If you would prefer to use flat-rate boxes (whether Priority Mail or some other carrier), then you would need to disable our USPS.com rate lookups by deleting your zipcode from Seller Admin > Cart Shipping Settings. You could then define the Cost of various container types as your flat rate, then configure each product with what type of flat-rate box it ships in up to what unit capacity. However, we don't have any way to "upgrade" from one container type to another based on the unit quantity being ordered.