Shipping Issue

Here is a problem we were getting from the past, we made a fix and now the problem is on the other end of the pole:

1. In the past our website woo commerce pull out shipping charges from our UPS account and was at times charging cheaper than we were being charge in actual.

2. After a fix, now it is charging way over. For example:

2.1 product # 1 – shipping charge pulled out by website is $49.28 via priority Mail

However our fedex account actually charges $16.00 (we typically add $5.00 for handling fee as cushion) So a total charge of $21.00 to our customer.

2.2 product 2 – shipping charge pulled out by website is $104.70 via UPS Ground

While actual shipping charge by our fedex account $ 41.11 (we typically add $5.00 for handling fee as cushion) So a total charge of $46.11 to our customer.

Anyone know what settings I need to configure?