USB and LiPo power supply with charger
Do you really need 5V to be used in your uC? There are some available uC's that can be powered with 3.3 volts, which will eliminate the hassle of boosting the battery voltage to 5V.

Q1 is what cuts the supply voltage from the boost converter if you plug it in to USB. D1 in the circuit makes sense but I don't think it's a good idea to put it there. Diodes usually have a voltage drop of 0.7 V, which means that if you power your circuit using USB, your VCC will drop to 4.3V.

You are also correct about the Thermistor being on the Battery. LiPo batteries have a history of being explosive and unsafe, that's why the thermistor is required.

EDIT: So far your circuit is correct and based on the datasheets that you have given, you are using these circuits the way they are supposed to be used.