You can setup a reduced price on specific combinations using the Specific Prices panel located in the Combinations panel.
Once you have selected the combination you wish to apply a discount onto, click on the icon for the corresponding line to be created.
Then complete the information in each required field.
And finally validate by hitting the refresh icon
You can of course setup the same discount on multiple combinations simply by selecting them before creating the specific price.
The options are the same as for products in the main Specific Prices panel. See this article for more information.