I input voltages must within certain limits. Even if you measure their difference. And your Arduino and your voltages must have a common ground so that you can tell(measure) what the voltages are.
If those voltages are too much for Arduino you can use an instrumentation amplifier for that. It is a special chip to make voltage differences to start from ground. Like 11V and 12.23456V becomes 1.23456V.
Leif