When updating the price of an item in Sales Order, SmartClient Picklist does not display “Custom” in the drop down due to NetSuite WebServices limitation. However, you can try the following option, to set it to a custom price value.
In the Excel cell, enter [[-1]] in the price column and update the record. SmartClient will then create a Sales Order with Custom Price level. You can verify it by refreshing the record from task pane and see the “Custom” price level.