The Ubercart shipping modules for USPS, UPS, and FedEx all communicate directly with the shipping company to determine shipping costs. If shipping quotes return a value that you think is wrong, the likely explanation is that what is being sent to the shipping company is not what you think.
In particular, the most common error occurs when the "Package quantity" field on the product edit page is set wrong. The intended meaning of "Package quantity" is "how many of this item can you fit in one shipping box". If you have it set to "1", which is the default value, then you are saying only one of those items can fit in a shipping box. As a result, when a customer orders 10 items, Ubercart will quote shipping cost for 10 boxes. If those 10 items really fit in just one box, it will seem your shipping quotes are 10 times too high.
To fix this, edit each of your products and change "Package quantity" to something more appropriate for that product.
If you have turned on the "all in one package" setting for the shipping method, it only applies to orders that have more than one kind of product. Since one kind of product knows what kind of package it goes in, the package quantity is used to determine the number of boxes needed.