I mixed the 2 chocolate flavors of ON with water all the time and it tasted good. As long as you don't add too much water, it tastes good. Ina have to hold my nose when I drink this "Delicious" Strawberry...but even the aftertaste is :x
Yes, you understand the TDEE correctly. As for putting moderately active on the site, I think that's wrong.
I have a desk job as well and even though I go to the gym 3x a week, I still put my activity level as sedentary. If I were in your position, I'd put the activity level to Sedentary on the IF site if you want to lose weight.
As for macros...losing weight is calories in vs calories out in the simplest form. Therefore, as long as you burn more calories than you eat, you will lose weight.
As for programs, I didn't like MyFitnessPal...I use Calorie Counter.