Hello Jorge,
To achieve a timekeeping accuracy of say, one second per day, the reference frequency error will need to be within 10 parts per million (ppm). Using a watch crystal as an external reference would achieve this accuracy only if it is trimmed with a trimmer capacitor. However, the method of adjusting the trim setting is likely to be by "trial and error" - not very convenient or quick.
With direct frequency measurement of the reference, the capacitive loading of the measurement probe will cause errors, and you would need a frequency counter with 0.1Hz resolution. Setting the output of a TPM channel for a specific period, and using a counter with period measurement capability, and with the period averaged over a number of cycles, may give more successful results.
Another approach is not to trim the crystal at all, but to automatically apply a time correction whenever the accumulated error reaches, say one second. The actual error, which might be 100 ppm or more, could be initially determined by measurement of TPM output period, as mentioned above, and would need to be stored as a non-volatile parameter.
Regards,
Mac