What is the proper way to measure an external supply like a 9V battery which is not connected to the controlling part (micro-controller) of the system. Take an external 1-Channel SAR ADC with SPI interface like MCP3001 and a micro-controller which has its own supply. I see we must divide the 9V first to 5V so the MCP3001 can properly handle it. But where to connect the VREF pin of MCP3001? Can I connect it to VDD like usually? Also do I need a galvanic isolation?
Since the MCP3001 doesn't have an internal reference voltage source, you will have to supply an external reference voltage that your input voltage will be measured against.
Depending on the measurement accuracy required, you can either use your ADC's supply voltage or a dedicated voltage reference like these. Either way, the accuracy of your measurements will depend on both the ADC's accuracy and that of your reference voltage.
Also remember to adjust your input voltage divider to scale the battery voltage to the range between 0 V and Vref (which might be lower than 5 V).