Always survey before you fly. This way, if you bump the GCP while measuring, there isn’t a difference between the measured GCP and the photographed GCP.
If you for some reason need to measure after the flight, then make sure that GCP’s are absolutely fixed to the ground with screws or nails, especially the center.
The best thing to do is to measure before flight (when setting them up) and then again after the flight, and then run a Network Adjustment on them (using a capable processor like EzSurv, or simply by averaging the 2 measurements) . Then you also account for changing satellite geometry etc, setup errors etc.
Why collect for 20 mins on the first and then 1 minute on the other?
Remember the height accuracy of an Ultra Rapid NRCAN PPP solution is around 20 cm. The Rapid is around 10 and Final is around 3-5, if my memory serves me correctly. So, if you need absolute accuracy, you have to wait the 16 or so days for the final product.
You dont have a nearby CORS station instead?
While this software is awesome, also try the Emlid Studio Beta, it provides a more integrated Work Flow.
As a final note, remember to transform the ITRF14 from NRCAN PPP to the appropriate system, otherwise your absolute coordinates will not be exact on the ground.