In Merchanter you can negotiate a deal for the whole order as well as setting prices and discounts for individual lines.
To modify the whole order value you can choose to click on the Total fields in the top right corner of the Edit Order screen.
Select the VAT inclusive or exclusive total figure depending on which one you wish to work on.
In the whole order discount window you can see the current value of the order and enter the target value you would like to achieve. This will show the revised margin based on your entry.
Once you have a value you are happy with you can choose how to apply it to the order:
Spread Discount - applies a percentage discount to all the order lines in order to achieve the total you are after.
Discount Max Value Line - applies a percentage discount to the order line with the highest value, leaving the other order values undiscounted
Whole order discount - adds a whole order discount into the totals of the order
Click 'Apply' to make the changes to the order.