Shopify shipping - weights not always consistant

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Hi Shopify people!  I am wondering if there is a workaround for the problem I am having.  I cannot seem to use the shopify shipping program as I have thousands of small products, all different, all weighing different weights.  I offer flat rate shipping and have been printing shipping labels off the Shopify site as it would take too much time to load all the weights for each product.  Is there a way to enter the box weight for each box before shipping, through the shopify portal on each individual package?  to clarify, each box is also a different weight, no two boxes are the same weight and I am using about 4-5 different box sizes.  So basically before each box ships, I weigh them individually and process the package on the freight companies website directly.  I would like to do this through the shopify site to take out the possibility for error on address however.  Any ideas?