The 90 day rule appears in Schedule 8 of the ANO. The requirements for logging flights appears in Art 28. You will note that there is no legal requirement to log take-offs and landings, so how do we ever know if a pilot is current? Even if you have 3 flights logged, there is no guarantee of how many take offs or landings you actually performed. Think how many flights a FI does where he does not land or take-off. At the end of the day it must be based upon trust, the onus is on anyone disputing your claim, to prove otherwise.
Maintaining currency is fairly straight forward, you need 3 take offs and landings in 90 days, you are not required to log them. How you obtain them does not matter so long as you do obtain them. If you are outside the 90 days, you either do them solo or take an instructor along if you are not happy, as the only way you can have two crew members in a SPA is for one to be an instructor. That way you comply with Sched 8.