Power rail design from Li-Polymer battery chip output
IMO the two main question would be :

1) What microcontroller do you use? You might be able to use it at a lower voltage, maybe by decreasing the clock frequency. This would simplify your problem a gread deal.

For example if you want to use an ATMega, you may power it with as low as 1.8V if you keep the clock frequency at or below 4MHz. It will also be happy at 8MHz with much less than 3.3V. Then you can power it straight from the battery/power manager chip; not using a regulator at all will give you some significant battery gains. 

2) What is the 3V3 part's lowest rated voltage? Depending on that, and the possible gains you'd make by not regulating the mcu voltage, you may be able to just discard the last drops of juice from your lipo for the same battery life (there is not that much energy left when it drops below 3.3V anyway...  plus, that'd be healthier for the battery), and get rid of the step-up to 3.3V altogether. Now a LDO regulator might to the job. No switching regulator means less noise ; less parts, less power usage, less volume/weight and less price also might mean a possible bigger battery...

In order to make the right choices you'd need to specify the specifications of the parts you'd use. But using an unregulated voltage for most of the circuit, including MCU, and regulated voltage for only the 3.3V parts has many advantages.