I watched a YouTube video on it just now.
Basically they said to just leave a window open (the guy had 16 open) and PT3 will grab them.
This doesn't work very well with PokerTracker 3. PokerTracker will import up to a maximum of 30 observed hands. Then it locks. The only way to have it start importing observed hands again is to wait 30 minutes, close the software, and run it again. So don't believe everything you see on YouTube.
As for the legalities of this, I believe HEM was allowing unlimited data mining. source
PokerStars has said:
The actual guideline issued by us is that a third-party program can import up to 30 observed hands per SESSION (not per table). We define a session in a particular way so that a player cannot leave their machine unattended and use the third-party program to datamine, or do so with the assistance of scripting.
...You can use any permitted third-party program to observe up to 30 hands per session.