Don't worry! TimeTracker is aware that humans get distracted (er, multitask), and TimeTracker only records activity for the active application. So, it's okay to have multiple windows open. TimeTracker will ignore whatever's happening in those other windows.
Side note: It's okay to walk away from your desk without closing windows or hitting 'pause'. TimeTracker looks for what you did most each minute. If you walk away from your desk for 20 minutes...TimeTracker sees no activity and therefore records nothing. When you return, it picks back up. Automatically!