How to configure GPIO pins as digital outputs on LTC6804?
This is done by appropriately setting the bits of the CFGR0 register (see table 36): The five upper bits (named GPIOx) are used to configure these pins. If you write a 0 in them, the correspondig GPIO pin will be actively driven low. If you write 1 (default value), it will be in high-impedance state (see table 46).

These PINs are open-drain (see page 31). So, if you want to use them as output, you need an external pull-up.