Work log timer helps you to determine the amount of time spent for a work more precisely. You can hide and show issue timer any time you want. When it is visible it remains on the bottom right hand side of the page and shows active issue and how much time passed since it is started. When you press the stop button, "Work Log Dialog" is opened. Issue, time spent, and start date fields are pre-populated from the timer but you can made any adjustment you want on the dialog before actually submitting the work log.
You can view list of all timers for the issues matching a JQL using 'Timer Dashboard Item' if you have permission to view issues.
Once started for an issue, it will continue to count even though you browse other issues or pages or even when it is hidden, until it is stopped or paused. You can't start another timer for another issue until you stop the current one because it is not possible to work on more than one issue at a time.
To hide the timer either use the "Show/Hide Timer" action from the main menu or just click on the cross icon on the upper right of the timer. You can show timer from the same "Show/Hide Timer" menu item at any time.
Work Log Timer and JIRA Workflow Transition Integration
During any workflow operation if there is a "Log Work" custom field on the transition screen timer value is automatically entered to "Time Spent" field, so you don't need to manually copy it and if you execute the transition work is logged to issue and timer is automatically stoped. This is especially useful if you force user's to enter a work log during issue transitions. Otherwise they will need to either manually cop the duration and work start from the timer to transition screen and stop the timer without entering any work log or they will enter the work log by stoping the timer and using "Log Work" dialog but in that case they will be promoted to enter work log again during issue transition. If you require a non-empty work log during issue transition they will need to by pass it by entering "1m" or similar work log.