The shipping look up in power store will not support a different package dimension for each item.
you can edit the code in the webassist/plugins/shopping_cart/calculate_shipping.php page to change the dimensions that will be used.
for fed ex, the code is around line 136 - 138:
$Shipping_PackageArray[$Shipping_PackageIndex]["PackageLength"] = "12";
$Shipping_PackageArray[$Shipping_PackageIndex]["PackageWidth"] = "12";
$Shipping_PackageArray[$Shipping_PackageIndex]["PackageHeight"] = "12";
you can change this to use the dimension you would prefer.