Adding FedEx

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We've been using Shopify for about 2-3 years. We have always used UPS and USPS but have recently added FedEx using PlugInHive.
We've run into a few snags. For one we cannot see FedEx listed but the customer can. 
We want to use their One Rate box on some things but it seems to be very complicated in trying to switch around to different boxes. 
We us approximately 50 different box sizes and the weights can vary greatly ranging anywhere from 1 pound to 50 pounds. 
I need things set up where I can pretty much use whatever box I need.
Should it just be set to "weight based" shipping? 
Does anyone have suggestions or tips for dealing with adding them on? 
Is there a better way than using PlugInHive?