To add additional charge(s) to Quotation or Sales Order, you'll need to setup Additional Charges in Company Settings > General Setup > Additional Charge and create additional charge(s). 

In Sales Order or Quotation, click on Additional Charges  to add the charge(s) and click apply, you can setup additional charge type in the App settings

You'll be able to add additional charges to the sales order even if it's already delivered but not yet invoiced. Open the Sales Order, click Edit and add the additional charges, then save. 

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