The rule is simple: FAIRTIQ must be active when travelling, and stopped when not travelling.
FAIRTIQ will sell and updates tickets as you travel. The number of check-ins and check-outs has no influence on the final price: the system might combine two journeys if the total price is lower than the prices for the two individual journeys.
If you are connecting between train/bus, we recommend keeping FAIRTIQ active (max. 25-30 minutes).