Hi Jessica,
What you would need to do is use the Amount column to store your
'amount after discount' and just use another column to store the amount before
discount. This way the subtotal will calculate correctly and be linked to the
correct QuickBooks field.
-Michael 
										    
									     
									    Michael Melo
Product Manager
Method Integration Inc.
Website: http://www.method.me
LinkedIn: http://www.linkedin.com/in/MichaelMelo