Need some help understanding calorie counting

The process is a simple principle. So not sure at what level you are asking for help.

You burn calories through the day in your activities.

If you eat as much as you burn, you maintain weight, less you lose, more you gain.

MFP estimates your daily burn based on YOUR selection of Activity Level - hopefully was right.

MFP calculates how much you should eat by subtracting some calories from that daily burn if you selected lose weight - hopefully it was reasonable rate you selected (I'll tell ya right now your body is under stress with that disease, you likely can't take what would be a reasonable deficit for others that have a generally healthy body).

That base eating goal includes no exercise - so when that is done you log it and MFP lets you eat more because you burned more. Life lesson there. Do less you eat less too.

So it's really a matter if hitting the simple principle.
Input what you have done to burn calories.
Input what you have eaten by weight to add calories.

Reach the goal that MFP spells right out for you to eat.

There are some nuances past that. But that's the basics.
Like log everything you eat by weight.
Confirm the entries are correct to nutrition labels, or say USDA if fresh items.

I agree. Set your diary to open and maybe we can better understand what you’re asking.