How do you account for negative variations in a logged recipe?

Three options:

1) Log the meal as usual, then log just the particular ingredient (cheese, in this case) from the database or your frequent foods or wherever, but log it as -15 (negative 15), and MFP will enter it in your diary with negative values for calories and other nutrients.

2) If you only track calories, not other nutrients, and you don't normally eat this cheese outside of the saved meal, so it would be a pain to find it in the database, you can just log the meal as usual, then use "quick add calories" to log -60 calories. If you want, you can make a note in the "Today's Food Notes" section to account for the negative calories.

3) This is probably more than you want to deal with this time, but going forward, I would suggest using the "my meals" function instead of the recipe function for "recipes" that are single serving (which is what this sounds like), so that you can adjust quantities or even substitute different ingredients (say, blueberries instead of strawberrries, or 2% milk instead of 1%, etc.) The first time you make the single-serve recipe, you just log the ingredients in your diary as usual, then you save it as a meal using the "quick tools" menu under the meal. Next time you eat it, you log the meal, and all the individual ingredients show up in your diary, and you can adjust quantities or make substitutions without affecting the saved meal.

I find the "my meals" function very useful for things like smoothies and oatmeal, that I mix different amounts of different things into each time I have it. After I log my saved smoothie or oatmeal "meal," I add anything I may have used that I never used before, like the first time I used defatted peanut powder (like PB2) in a smoothie. Then I save it, replacing the old saved meal. Only then do I delete any ingredients in the saved meal that I didn't use, or change any quantities.

I also find the "my meals" function for my favorite restaurant (including fast casual, fast food, carry-out, and food truck) meals at places I eat at regularly but that have no posted nutritional information, so that I have to "deconstruct" (i.e., guesstimate and log as their constituent parts: 6 oz. chicken breast, 1 tbsp. olive oil, 120 g. asparagus, etc.).

And I have "my meals" entries for the available ingredients that I use at "pick-and-choose" restaurants, etc., like Chipotle and similar "assembly-line" fast-casual places, the burrito cart near my office, "salad bar" with the ingredients I tend to use at salad bars, and Coldstone Creamery ice cream with the flavors and mix-ins I tend to get. For example, the Chipotle "my meal" includes all of their ingredients that I eat, and none that I don't (black but not pinto beans, sour cream but no cheese because I can't taste it with all the other stuff so it's not worth the calories, and I only like the shredded meats and the sofritas, so no steak or chicken in "my meal"), so after I log it, I just delete a few protein choices, and the guacamole if I didn't get any, and I'm done.