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. 

To apply this settings to your AC in Sales Order, go to Company Settings > Basic Settings > APP SETTINGS > SALES ORDER > Additional charges calculation> Include additional charge to item line > CIF/FOB Calculation. In the sales Order, select CIF/FOB calculation in the AC modal and enter the AC for your products then click Save.