It sounds like you are doing things properly. As long as you set your GoPro to take the images every 2 seconds you should be good. You will have to make sure that you take out the images from before and after takeoff and from the ascent and descent. Only upload images that were taken at the cruising altitude.
The imaging locations that are on the flight planner are just there as a guide. As long as you have something similar to that, you should be good.