You should try on of these:http://www.sparkfun.com/products/11231
If you want to integrate it to your board you can use the schematic and eagle files at the bottom of the page.
The TPS61200 (~$3 at digikey) can replace your regulator, provide battery protection and provide a consistent voltage (3.3 or 5v) to your board right through the voltage range of the LiPo (e.g. 2.6 - 4.2 volts).
P.S. If you are running out of I/O have you though of the ATmega32u4 chip? (Arduino Leonardo) or a quantum leap to the Atmega2560?
The AtMega32u4 also has built in USB so you would not have to use V-USB. The Atmega2560 would use less power than using two Atmega328s yet provide you with many more pins. The extra memory would allow you to use better networking (e.g. the excellent open source RFM22b meshing library at http://www.open.com.au/mikem/arduino/RF22/
) if you were prepared to switch transceiver to the RFM22 ($4.50 from Hope).
It is a bit powerful but is highly configurable to save power.