LiPo Battery: series to parallel charging switching circuit
The charge controller is described as a "Miniature Single-Cell, Fully Integrated Li-Ion,
Li-Polymer Charge Management Controllers".

This means it can charge 1 (one) Li-Ion cell. If you want to charge two then buy another. 

How to wire two together? It seems that the prog pin might help: -


  The charge management controller can be disabled by allowing the PROG input to float.


Will this allow you to then connect the two batteries together without damaging the charger chip? It appears so but it's not absolutely clear. Possibly, by having a schottky diode connected from Vbat terminal to Vdd input power terminal this can be safely achieved. You will need to investigate this yourself.

So, if this works you can use two back-to-back MOSFETs (wired like a solid-state-relay) to link the two batteries together and then this combined battery can feed your boost circuit.

Regarding your circuit, M1 is shorted out and you need two charge controllers so I'm not attempting to analyse it further.