To configure a combo deal, you should create a new product to represent the combo, with the combo selections as product variants. The combo product should have the price of the combo, and the product variants should all have zero price. The products that are available as part of the combo should be linked to the variant values.
You want to create a combo deal for $10, where the customer can choose one muffin and one coffee.
You create a product called "Combo" with price $10. Then you create a product variant group for muffin selection, with a variant value called "Blueberry Muffin". Then you link the pre-existing "Blueberry Muffin" product to the "Blueberry Muffin" variant value. This will make the "Blueberry Muffin" variant value take on the printer locations and extras of the "Blueberry Muffin" product (but not the price).
You create variant values for all the available muffins in this way. Then repeat the process for the product variant group for coffee selection. Finally, you add the two product variant groups to the "Combo" product.
Note: If you want the combo selections to contribute to the usage report and stocking quantity, then fill in the "Usage" column. If product X is linked to variant value Y, then the usage number should be the number of product X used for each variant value Y used.