I am using FogBugz as a tool to give us "a look into the future". The program takes our work hours, the tasks for a release, assigned developer's estimate against that task, and the developers tendency to under/over estimate, and tries to come up with a probability of making the release against a range of dates in the future.
Now since FogBugz takes into account the work hours, it assumes that the developers will put in the hours into the tasks they are assigned, which is not true in XP because the earlier decision of the pair was to work on one of the developers' tasks together.
Does this mean that I cant use FogBugz for estimates when doing pair programming?
What I would do in this case would be to have each developer estimate each of his cases for the release expressed in working hours it will take to complete it while pair programming (that is, time spent with a partner actually working on that case). Then figure out about how much time you spend pair programming on your own tasks vs. on someone else's tasks, and set your "% time spent on FogBugz tasks" on your Working Schedule to the approximate percentage of time you spend on your own tasks.
Then, when you're working on your tasks, mark yourself as Working On -> case ID, and when you're working on someone else's tasks, set Working On -> Nothing.
There are actually a lot of different ways to get get this to work (and the other answers here might be better depending on the circumstances), but that's how I would do it.