Negative input voltage on Isolated Differential ADC
The first configuration will work, provided that the ADC has true differential inputs and the input voltage is floating relative to ADC ground. 

In the circuit below, consider the loop formed by Vdd, R1, Vin and R2 at various input voltages,


Vin is 0V:- R1 and R2 are effectively joined in the middle, each resistor drops 2.5V (Vdd/2) so the ADC gets +2.5V on both inputs.  
Vin is +5V:- Vin opposes Vdd leaving zero volts across R1 and R2, ADC gets +5V on Ain+ and 0V on Ain-.
Vin is -5V:- Vin adds to Vdd so the total driving voltage in the loop is 10V, R1 and R2 drop 5V each, ADC gets 0v on Ain+ and +5V on Ain-.   


One potential issue is that current is fed into Vin (through R1 and R2) even  when it is 0V. If Vin's source impedance is not very low then a significant offset voltage may occur (ie. ADC does does not read zero when it should).







simulate this circuit &ndash; Schematic created using CircuitLab

The second configuration will not work, because despite being attenuated the negative input will still go below ground. To fix it you could double the value of the resistors going to ground, and add same value resistors to +5V. This will result in the same attenuation, but provide a '0V' reference of +2.5V which the inputs can pull up and down. Once again, this will only work properly if Vin is floating relative to ADC ground (or at least does not pull either terminal below -2.5V or above +7.5V).