Planning a flight with Top Meteo weather overlay works exactly the same as without it. Except it adds context to your planning. The basics about how to plan a flight with Seeyou are here. With the Top Meteo overlay you are actually planning today's flight (or tommorow's or the day after's) with real soaring weather forecasts from Top Meteo. The plan is to plan as much as your flight as you can in the areas with better forecast:
The flags with time stamps tell you where you are forecasted to be at the given times during the day or when you are going to reach a turnpoint.
The start and finish flags superimposed on top of each other. For as long as the finish flag is green the forecast says you can make it. As soon as it turns red the Top Meteo calculation predicts outlanding at that spot. Note that the finish time calculation already includes final glide altitude and distance you are expected to achieve. Note that the task distance counter also glows red when the task is seems too long to finish in time according to the forecast.