In the +6.144V range, the ADC result accomodates this range, but, the input to the GPIO should be limited to VDDA -250mV and VSSA +100 mV.
Applying negative input in differential mode, means that the positive input of the ADC is at a lesser voltage than the negative input of the ADC, while still obeying the limits of the GPIO which is VDDA -250mV and VSSA +100 mV.
As Sampath indicated, you should not exceed the lower (0V) and upper voltages (VDDA). You can go a little above and below them but I wouldn't encourage it.
You are correct on being somewhat confused. The Differential input option of +/-6.144V is a bit unachievable. At best with VDDA at 5V you can achieve a differential reading ADC range of 0V to 5V. which would be less than 1/2 the resolution available to the ADC.
I can make a ADC front-end recommendation if you can describe the characteristics of the signal you are trying to measure.
In general, ANY signal above VDDA (5V) needs to be scaled down. One scale down technique is to use resistor dividers.
Any signal below VSSA needs to be bias upward. This can get tricky.
If you describe the input signal to measure, we in the forum will try to help design an analog front-end.