You should use one of these solutions

- op-amp in differential circuit (LM358 - cheap and popular rail-to-rail op-amp)
- external differential ADC (MCP3421 - i2c, differential, slow, accurrate, easy to use but slow)

to measure differential signal with ATmega328, because this microcontroller ADC has no differential feature.

Trying to connect your signal source may be very bad idea (depending on your signal source).