I’m trying to make a point system to run along side xoops. I would like to know how to make a new field in user profile so that I can make the amount of points update from my point script. I would also like to know how the cookie encryption works or how to validate the users. This is so when they complete a task my script know who to add the points to and the user can find out how many points he has. Is there something that I can read that will explain to me how the xoop's code works?

You may also search for the UserPoints module. This one is maybe a good start for you as it already counts points from different things.