Raw goes through the voltage regulator, so you won't want that. If it is less than 5V hook the battery up to Vcc.
How can I use a led on Arduino Pro Mini 3.3v to indicate low battery(so I can change it before it dies).
You can self-detect the power level by using a technique invented by various people, a copy of which is on this page:
Scroll down to "Detecting low voltage".
Of course the LED will itself use power, so you probably want to flash it briefly.
Thank you Nick for you advice!
I need to change the battery to a Li-PO One, 3.7v, so in this case it will be a problem to put it straight to VCC, maybe I will recharge it directly through a Li-PO charger, when the battery is still connected to the system. There will be like 4V, which is not good for BMP085 Sensor or for the Ftdi chip with 3V3. Is write in this case?
Thank you,
Razvan