You may want to take note of the following observations I have made from using this software.
1. The pokemon are downloaded from the Internet via SpotPass, so keep your Nintendo 3DS on with wireless enabled with connection to the internet (for example on and in range of your wireless router's signal)
2. Scanning the Cobalion, Terrakion and Virizion AR Markers will cause you to receive those Pokemon immediately
3. Scanning other AR Markers will increase the odds of recieving that Pokemon through SpotPass.
4. I have also taken notice that I tend to receive 1 in the morning, 1 during day and 1 in the evening, they aren't given all at once.
5. The software doesn't seem to check for Pokemon while playing a game.
1. you don't have to turn your spotpass on all the time, you just have to turn it on each day (when you want to receive the data, and it only takes about 10 sec.), the day is count with UTC time, so each day is count from 00.00 UTC to 24.00 UTC
2. there are 6 pokemon you can receive only just scanning their AR marker, those pokemon are: Victini, Cobalion, Terrakion, Virizion, Reshiram, and Zekrom
3. most likely, but not always
4. you can receive all 3 pokemon ech day in the same time, just go to home screen and resume the pokedex3d (no need to close the pokedex3d apps.)
5. you can receive the pokemon data while doing anything including play a game, as long as your wireless function is on and you're inside the wi-fi range.