Depends what you want to do with it.
You can use it to analyse your play after the game, in which case there is no need to open it until afterwards.
Or, with a suitable HUD, such as GTPlus, you can use it to show you some stats on your opponents during the game. If doing that, open it ten or fifteen minutes after you join the game (the stats are no use until you`ve gathered info on at least 20 hands).
Finally, you can use it to datamine. To do this, open PT and open (as an observer) 3 or 4 tables at the limits you`re going to play. Then go and get a coffee. Come back in half an hour. PT will have analysed the play at the tables and you can take a seat at one of them armed with a read on the opponents, right from your first hand.
You`re not stupid, m8, but PT is very complex. Definitely read the help files, search for relevant threads here on CC, and look at www.pokertrackerguide.com