Doubt is for when it sounds like they are withholding information. Like if you ask a guy, "Do you know where Jim went after work?" and he replies "Err...no. I saw him leave, but he didn't say where he was going" and looks nervous while saying it, then use doubt. Lie is when you straight up know they are lying about something AND have the evidence to prove it. It's a good idea to glance at your evidence (you can even do this when the Truth/Doubt/Lie prompt comes up).
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Currently playing: Assassin's Creed: Brotherhood and Chronicles of Riddick: Escape from Butcher Bay