How to apply tax in the markup amount in BUSY?

Yes you can charge the taxes only on the markup value by following these steps:
Step 1: Make sure markup feature is enabled in your company
Step 2: Then go to administration menu
Step 3: Then click on masters 
Step 4: Afterwards click on bill sundry
Step 5: Then click on modify or list button then open the cgst,sgst and igst master one by one 
Step 6: Then copy the master by pressing f12 key 
Step 7: Then click on duplicate master
Step 8: Afterwards change the name of copied bill sundry in new master as cgst for markup as recommended and same for the sgst and igst simultaneously
Step 9: Then click on net bill amount or items basic amount option as required available in the right screen of bill sundry master
Step 10: Then click on selective calculation option and select this option as y to enable it 
Step 11: Then tick the markup amount
Step 12: Then press on ok button then save the changes
Step 13: Afterwards go to transactions menu and make the invoice and use bill sundry of cgst,sgst,igst for markup as per the requirement
Step 14: Then it will apply the tax on the markup value