How can I setup a discount item where I can enter the amount of the discount at the time of the Sales Order? We're not importing our sales data at the order level, but total $'s by item for the entire month, so the amount I need to enter for the discount will never be a flat $ amount or a perfectly rounded %.

Just create the discount item with a rate of 0 Then when you add it to the sales order you can specified whatever amount of discount you want to