you do have it set properly to use 1 package for the entire order, but you are overriding that by seting the quantity to use the cart quantity.
change:
$Shipping_PackageArray[$Shipping_PackageIndex]["Quantity"] = "".WA_eCart_FormatNumber($eCart1->DisplayInfo('Quantity'), true, 1) ."";
to:
$Shipping_PackageArray[$Shipping_PackageIndex]["Quantity"] = "1";