Shopify/CustomCat Shipping pricing mismatch

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We had a purchase made and the invoice reads as follows;

T-Shirt -                      $29.99

Shipping -                   $13.90

Total to Customer - $43.89CAD


We have a custom cat integration for fulfillment and was under the impression that the check out was handled by them - apparently not ( this is our first store  brand new to this)   How is the 13.90 getting added and or calculated and added to the checkout? Where is that controlled and how does one set up the shipping costs within the check out of shopify??????????? Please any help or light you can shed on this would be valued. 

For more context and hence our confusion: Custom cat charges 6.50 usd which is roughly 8.64 CAD (our store is in CAD) - so why was the customer charged 13.90 how was that calculated added to their order?????

$6.50USD converted to CAD is $8.64

our customer was charged        $13.90

for a difference of                          $5.26 extra they were charged??????? (super confused)