The battery will go to a step up circuit to 5V and feed the atmega, I want to alarm the user when it get''s to a point that it should be charged again. As the processor might turn off due to the low battery I guess is better to put a resistor in series to to make sure that that case is also covered!
There have been some comments about alternate methods of powering the Arduino and monitoring the battery, but in case you want to stick the what you've stated above, note the following:
The difference in voltage between a LiPo cell at full charge and discharged is quite low (about 4.2V-3.2V=1V). To accurately determine that your battery has reached the desired "alarm" voltage will require your ADC reference to be quite precise a stable.
If you're using a voltage boost circuit to provide 5V Vcc and using Vcc as the ADC reference, and you're software calculates based on a 5V reference, the actual output voltage of the regulator circuit will have to be quite close to 5V (probably within 1%) to obtain an accurate enough battery reading. Otherwise, you may end up giving the "alarm" long before the battery needs to be charged, or too late.
If you can't guarantee a precise absolute known value for the supply/reference voltage, but for a given unit this voltage, though not necessarily exactly 5V, is always the same when the battery reaches the "alarm" voltage, you can calibrate each individual unit and store the necessary calibration values in EEPROM. You might want to do this even if you're making only one unit. For multiple units, each one will need it's own separate calibration, though