You will not be able to catch Moltres/Zapdos/Articuno right away. The legendary birds will wonder around the Kalos region and it is your job to hunt them down. To locate the birds, you will need to encounter the Pokemon at least once. After that you will be able to track the location of the Moltres/Zapdos/Articuno through the Pokedex.
Open your Pokedex and select the National Dex. Scroll down to find Moltres/Zapdos/Articuno and select the Pokemon. You will find a section that shows the map of Kalos. A red line indicates where the Legendary birds is currently located, go to the location and search the grass to encounter the Pokemon (indicated by a special flash). The bird show flee automatically thus you must repeat the process. After a number of encounters, the bird will rest in the Sea Spirits den (you can use the Pokedex to locate). Their you will be able to capture the Pokemon.
Basically, that is how you will know where Moltres is, there isn't anything known about how to determine where it will fly to next, whether it be a set order or what. It appears to be random. Source.
I'm not sure if this helped you answer your question, just tell me and I guess I'll hide it. =/ Hope I helped anyway.