In case you still need answers...
"When the default shipping appears in ship-in-cart, the shipping total is double what the ups ground amount is."
I was also getting this problem after installing the "ship in cart" module however my ups.xml file was already updated with the "reset quantities" code as outlined above. After researching and working on this issue for many hours, it appeared that this problem was linked to the "Dimensions Support" in the UPS module which was apparently converting 1 item purchased into 2 packages. Since I did not really use this feature, I changed my selection in the "Dimensions Support" from "With product dimensions" to "No" in the Admin panel. So....
Go to the Admin control panel
Click on "Module">"Shipping">"United Parcel Services (XML)"
Click on "Edit"
Select "No" under the "Dimensions Support" category
Click on "Update"
The above settings should resolve the double counting appearing in the "Total Cost Estimate" for the ship-in-cart module.
Good Luck!