You're showing a new employee how to use a computer program. He seems to be confused by it, but you don't think it's that difficult to understand. You want to reassure the new employee, so you say:
Once you get to know it, it's not that hard.
This means that the second event happens very soon after the first event. The second event naturally follows from the first one.
This means to gradually start to know more about something (like a computer program). It's also used with people:
Once you get to know Chelsea, she's actually pretty nice.
This means something similar to "not very". In the example above, the new employee thinks the software is difficult, but you want to say that it's not as difficult as he thinks. So "not that ___" means "not as ___ as you might think".
This is a more casual way of saying "difficult".
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