If you sometimes have to modify prices during an order, but you are unable to do it with upcharges you can use the Price Modify feature.
This allows you to make a one-time price change of a product, specific to the order.
To Activate Price Modifying
Go to the Settings > Admin > Workflow > New Order Page.
Enable the "Allow Staff to Modify Prices on an Order" option.
Press the Update button below.
To Use Price Modifying
Create a new order as normal, adding items to the basket.
Click on the item name in the basket and a Modify Price box will appear.
There you can increase or decrease the price.
This will only change the price of the product in this order, and will not affect future orders.