The dimensions for the box are set on the confirm page at lines 422 - 424:
$Shipping_PackageArray[$Shipping_PackageIndex]["PackageLength"] = "12";
$Shipping_PackageArray[$Shipping_PackageIndex]["PackageWidth"] = "12";
$Shipping_PackageArray[$Shipping_PackageIndex]["PackageHeight"] = "12";
and on the pp_confirm page at lines 148 - 150.