How to detect low RTC battery with low extra battery load?
You can't connect the battery directly to the microcontroller, beacuse when the microcontroller power is off. battery current will flow through the 
microcontroller's ESD protection diodes, so some sort ot switch is needed to 
block that current when the microcontroller is powered off..







simulate this circuit &ndash; Schematic created using CircuitLab

In the top diagram A MOSFET is used to switch the battery current off when there is no power. to read the battery coltage output low on 'sense' abs high on 'control' to charge the capacitor. then set sense to inout and set control to low to turn the mosfet on, you have about 10 milliseconds to read the voltage before the MOSFET will turn off..

In the bottom diagram a diode is used instead, to read the battery voltage set control to high, the voltage on sense will be about 500 mV higher than vbat, while the diode is conductiong a small current will flow into the battery, so use it sparingly. you could possibly us an internal pull-up on the sense pin instead of R2.

In motherboards the clock itself has an indication that the the battery is low. check your RTC's datasheet. it may also have that feature.