I've been with shopfiy a few months and was just using the default rates they get from CP. After comparing my commercial rates i noticed mine were lower so i added CP as a managed carrier however now when customers place an order the shipping cost they pay is what Shopify fetches from my CP account (although it seems a bit low) however what i pay is the shopify rate...I've had a ticket open for over 2 weeks with no resolution. Has anyone else had this issue? I'm losing $1- $2.50 an order on this.. See picture for an example
Since this is an old thread, I hope you would have found a solution for this issue. So, I'm answering this query so that it would be helpful for others with similar issues.
In this case, the best method would be to use your own Canada Post account along with the Multi Carrier Shipping Label app. The app helps you integrate your own Canada Post account and calculate the rates using negotiated rates from Canada Post. Also, you can use the app to display your account rates at checkout, print shipping labels and also automate the tracking process.