Eating too much or too little?

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I am turning to you, dear community, for some advice surrounding food.. yes, food. Sigh

I have been doing fitnessblender workouts for some time now, got really into it in summer 2018 and in January 2019 I have bought FBabs Round2 which I have completed, after that I have started a 5 days challenge – burn fat/build muscle which I am one day away from completing and after that I am planning on starting FBabs Round2 again.

I am tracking all the calories, marcos, calories burned by exercise that I am supposed to add to my daily calorie intake so I don't undereat (I think) with myfitnesspal. I am eating no processed foods (only whole wheat pasta and very dark chocolate), I make my own whole wheat bread, I have tons of healthy recipes, nothing unhealthy. According to the BMR formula that is included in the FB program I am supposed to eat around 1964kcal/day, that is with moderate 3-5 day exercise (my basic BMR is 1267kcal). Myfitnesspal is showing me I should eat 1470kcal+calories burned by exercise.. that would be about 1750kcal/day.

I am 25yo, 160cm (5'25 ft) and 46kg (101 pounds) thin like a stick with a little pooch (skinny fat). In nooo way I could eat that much per day because sometimes eating 1300 is a problem to me because I feel like I am eating too much already. I have been doing intermittent fasting (8/16) for some time now but I feel like it is just making things harder as I cannot push all the food down in the 8 hour window. Today for the first time I am at approx. 1250kcal/day at my lunch time (2-3pm) only because I have eaten breakfast before and dinner and some snacks are still left.. but the app (that I sometimes want to uninstall so bad) is showing me I had already exceeded my daily fat intake ..and I am trying to up my protein intake lately, because I have read skinny fat people should eat more protein or bulk up more to lose the belly fat, but I cannot because foods that have protein also have fat (except for beans which I am trying to eat 1.19 pounds per week and it is still not enough).

I have thought of throwing every calorie counting out the window and just eat how I feel is right but I know I would be undereating according to everything else? Maybe I'm just not 'used' to eating 'more'? Also I have lost 2-3 pounds (1kg+) since completing FBabs2 (probably fat), and maybe I should just keep going like this and maaaaybe fat would be replaced by muscle?

Also I have purchased resistance tubes to 'lift' heavier as I cannot afford heavier weights (I have a few lighter ones in the house). I am sorry for my rambling but I am truly lost and I am very grateful if you took your time to read my issue. Hope you have a wonderful day

Edited