For liquid level sensing applications, you need to calibrate the container when empty and store the baseline in flash. This can be done during production and a user button or any other input method can be added to calibrate it on field. Upon every subsequent powerup, you can read the calibrated value from flash and then compare the raw count against the data that was stored to process the amount of liquid present.
If the baseline is not stored in flash, then on power-up you will lose the liquid level reading since, CapSense sets the baseline = raw count on power up.
I am attaching a project that shows the same with this response.
To measure the Cp, you can enable the self-test library in the component and use the CapSense_GetSensorCapacitance API to read the sensor's Cp.
I have shown this in the attached project as well.