This can be done from your Business Dashboard under the Online Ordering section. Click on offers. 

The auto-apply feature is valid if your offer meets the following conditions - 
1. Is a Percentage off offer
2. Percentage off on category 
3. Rs. off on category 
4, Is multi-use 
5. Is available on the microsite 
6. Is available on all items 
7. Is not a loyalty / referral offer 
If your offer meets these parameters, there will be an option 'auto-apply offer' that you can enable to activate auto-apply for your offer, as shown below. 
