How connect a open collector output to led and to GPIO?
If the ATMega328p is operated from the 3.3V supply, you can connect them directly, but you should enable pullup resistors in the ATMega, because the voltage drop of the LED may be high enough that the pins will not be reliably pulled up to a logic '1' when the outputs are off. 

If the GPIOs get switched accidentally to outputs, a fair bit of current will flow to the BQ so it might be more conservative to use a series resistor perhaps 470 ohms. The minimum (internal) pullup is 20K so that will result in an extra 80mV  or so of output voltage, not disastrous.