measure +3V and -3V through resistor divider and switch on/off by digital pins
When measuring a voltage that is higher than the maximum rating, the voltage of interest is tied to ground with a voltage divider. When measuring a negative voltage, you instead have to tie the voltage of interest to the positive supply voltage (study the answers to this question).

In theory you can use the internal pullup to spare one resistor, but I would consider this a bad practice and recommend using an external pullup for the following reasons:


a uC's internal pullups/-downs are not accurate and sometimes not specified
especially when measuring negative voltage, chances are that harmful voltage is applied to the adc (consider the default state of a gpio)
a pullup/-down is an uncritical component concerning its value and precision. Therefore they are very cheap