There is a list of packages defined for use across all webstores under your account. This list can be customized to whatever dimensions and weight limits you desire. Our system uses this list load all the items in a rate request into the smallest amount of packages possible.
For example if someone orders 600 individually wrapped pens, the packaging algorithm would not send 600 12in x 6.5in x 6in boxes with a single pen rattling around in each one. It would try to put those 600 pens into the boxes with other items that still have space in them or it would try to combine them into 1 box that fits them perfectly if possible.
It uses all packaging options at its disposal for all items in order to achieve the most efficient usage of packaging space available.
We then take this final list of packages and make a request to FedEx in batches of 100 packages (the max amount they accept at a time). We then add up the total of these rate requests for our final total.
Our system will use your FedEx account which means rates use your negotiated shipping rate and ships from the shipping origin address we have stored on your webstore account.
If you find that the rate coming from our system is not matching what you'd expect, you should try running the rate using the FedEx standalone tool to compare. https://www.fedex.com/ratefinder/standalone