The Working On menu is used to allow developers to inform FogBugz which cases they're working on at any given time.
FogBugz collects this data in timesheets, which you can edit at any time.
Keeping accurate timesheets provides important input to the Evidence-Based Scheduling algorithm (EBS). The more meticulous developers are at entering estimates and keeping accurate timesheets, the better the results will be from EBS.
To make it easy to track your time, FogBugz uses the developer's working schedule (Admin | Working Schedule) to stop the clock, automatically, whenever you go home, and start it again, automatically, when you come back in the morning. It also stops the clock during lunch breaks, when you're on vacation, etc., as long as you tell it when these things are going to happen. That way you only need to change the "working on" case when you switch from one case to another.
At any time, you can see and edit your current timesheet, or any previous day's timesheet, by choosing "Edit Timesheet" from the "Working On" menu. Use this feature to adjust times that were captured incorrectly.
If your schedule varies slightly from day to day, don't worry too much about entering precise times. The EBS algorithm doesn't depend on getting precise to-the-second data about everything you're doing.