If you want to add discount and tax in the order programmatically, here is the code snippet to apply discount and tax in your custom code :
$subTotal = 150;
$taxRate = .0825;
$taxAmount = $subTotal * $taxRate;
$shippingAmount = 10;
$totalAmount = $subTotal + $taxAmount + $shippingAmount;
$order->setSubtotal($subTotal);
$order->setBaseSubtotal($subTotal);
$order->setGrandTotal($totalAmount);
$order->setBaseGrandTotal($totalAmount);
$order->setTaxAmount($taxAmount);
$order->setDiscountAmount(0);
Hope this helps you guys!