If you want to play dual games, i.e. a little offline (with trainer) then some online (and you worry about it), it is best to restart your PC before heading online.
[Edited by Vlad_the_Bad, 6/22/2015 6:18:01 PM]
this has been the official CH stance for trainers for a VERY long time. if you want to be legit restart the game with no trainer.