How can I swap the sale and compare at prices?

By default, Frequently Bought Together displays the compare at price after the sale price when a product is on sale and the app is configured to display both prices.

This also applies to the bundle total amount as we can see in the screenshot below.

However, some themes swap the compare at and sale prices so that the compare at price is displayed first.

Frequently Bought Together automatically configures the order of prices for all free themes and some paid themes but you can always change the default preset at any time from the app preferences page if for whatever reason prices are displayed in a different order. 

From the Visual preferences, clicking on Prices section on the left, you will display the price options to change easily the preference 'Order of prices' to match your theme behaviour.
In the screenshot below we can see the Frequently Bought Together widget with the sale  price and original price swapped, that is, the original price is displayed first.