By default, the app considers the Compare at price as the base price while applying discounts or calculating shipping charges. For example, take a product with:
Compare at price of $39.99 and
Sales price of $34.99
For a customer in the discount group 'Wholesale' which has a percentage discount of 60%, the product will be available at $15.99, which is after a 60% discount on the Compare at price of $39.99.
Also, if there is a minimum purchase amount associated with the discount group to apply discounts or shipping rates, the app compares that with the non-discounted total by default.
For example, If the discount group 'Wholesale' had a minimum purchase amount requirement of 200$.
As you can see in the image below, a percentage discount of 60% will be applied once the non-discounted total amount is more than $200.
If you would like to change the default settings and apply discounts to the Sales price, here is an article to help you out.
Once the settings are changed the discounts and shipping rates will be applied to the Sales price as you can see in the images below.