This forum is to be used for all discussions pertaining to Obsidian Entertainment's Neverwinter Nights 2, the Mask of the Betrayer expansion pack, the Storm of Zehir expansion pack, and the Mysteries of Westgate adventure pack.
Nope, it doesn't affect your alignment at all, if you make the right choices. As a chaotic good character you don't even have to worry about chaotic points, so go ahead.
Without spoiling any of the quests I can tell you that there are pretty much good, bad, neutral, chaotic and lawful choices for all quests regardless of whether you join the Watch or the Thiefs.