That all sounds a rather round about way of powering the board.
So you have 3.7V LiPo battery -> LiPo charger (TP4056) -> Boost Module (MT3608) -> Vin - hopefully generating around 7V?
I think you can wind down the MT3608 to 5V and connect its output to the 5V pin. Hopefully somebody with more knowledge than me on power will chip in shortly and point you in the right direction.