It's common for Amazon to request that a shipment be split among multiple FBA warehouses. As long as it's clear which boxes need to go where, our freight forwarders can generally handle that.
There are three ways to go about handling these kinds of shipments:
1) Have the freight company arrange trucking to the separate destination warehouses (which, depending on their proximity, could be expensive)
The quote you get online would only be to one destination, as that's all the system will allow at the moment.
To get multiple destinations, notify us where the second warehouse is at the point of booking, and indicate it in the comments with your shipping details. That way we can simply add an additional trucking charge.
2) Use the Amazon delivery service offered by UPS (which can be a cheaper option for warehouses further apart from one another)
In this case, you only need to book a quote to the city from which you want UPS to begin their operations. So, for example, if you want the freight forwarder to bring the goods to their warehouse in NYC and have UPS pick up the goods from there, then just select New York as the delivery location to calculate a standard rate for that city.
Learn more about booking final mile last leg trucking to a UPS warehouse in that article.
3) Book separate shipments to separate warehouses.
This could be a good option if your warehouses/ destinations are on opposite sides of the country.
Additionally, if you have two 10+ CBM packages, it might be worth it to ship two separate shipments
If you let us know more details about your specific shipment, we can estimate the best options for you!