How to setup my Goals

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Hi

I am trying to gain muscle.

From doing research and talking to my personal training this is what I figured out.

Maintenance - 2620
Target Calorie Intake 2870 to 3120 for gaining muscle

Protein in Grams = 147 to 220
Fat 80 to 87(if I am at 3120 calories a day)
Carbs 318 to 391 or 364 to 438 (if I am at 3120 calories a day)

The numbers I am aiming for is

2870 cals
147 to 220 in protein
80 in Fat
Carbs 318 to 391

The thing that gets me with myfitnesspal goal system is the calories that I burn a day.

The numbers I listed was using BRM and Harris-Benedict Equation.

I put in that I am moderately active(working out 3 to 5 times a week)

Exercise

2 times a week on elliptical for 30 mins burning 175cals
3 times a week of weight lifting(one day with personal trainer)
- 7 min warmup on stair master (105 cals)
- 5 mins finishing up on stair master (75 cals)

So when I put in my goal the calories come out pretty close(2840) to what I listed above. However once I start adding exercise to it then the number goes all bad since the number(2870) that I listed already accounts for exercise(that's what the Harris-Benedict equation does).

Where myfitnesspal only accounts for your not gym hours. So if I put in what would be equivalent to my profession(computer programmer..what is sitting around all day). The the cal intakes changes to like 2500 and if I add all the exercise I do the numbers are all weird.

So how do I account for exercise. Should I add all my numbers in manually and calculate how many calories I just burn from exercise at the gym or what?