Let all the air out of the -ve chamber, set the pressure in the +ve chamber to your desired pressure, then pump the -ve chamber up to the same pressure once you've done that.
The -ve chamber is there to make the fork more supple in its initial travel. Running the -ve chamber empty, the fork will not react to small bumps very well at all. Running it too high and it will be very supple initially, but will eat into your available travel. The best bet is to match the pressures, therefore not eating into the travel but making it as supple as possible initially.