Is there a way to automatically apply discounts ?

Yes you can apply the discounts automatically in BUSY by following these steps:
For voucher level discount follow this:
Step 1: Go to administration menu Then click on configuration button
Step 2: Then click on tag bill sundry voucher wise option
Step 3: Afterwards select the voucher type ,series name and sale type 
Step 4: Then tag the bill sundry and save the changes
Step 5: Afterwards whenever you will select the same series and sale type for that voucher discount will be automatically applied in bill sundry
For item wise discount follow this:

Step 1: Go to administration menu Then click on configuration button
Step 2: Then click on features and option button
Step 3: Then click on inventory tab
Step 4: Afterwards click on items pricing mode in vouchers available at the bottom right
Step 5: Then select party-item-wise discount structure and select mode as mixed mode or any other as required
Step 6: Then save the changes
Step 7: Then go to administration menu again
Step 8: Then click on configuration button 
Step 9: Then click on party-item price structure
Step 10: Then click on voucher such as sale or purchase and configure the discount as required and save it 
Step 11: Afterwards go to the transactions menu and create or modify invoice in which you want to apply the discount at item level autmatically
Step 12: Then whenever you do the entry in item grid it will automatically calculate the discount as per the structure