Keep user interface running when main window closes - ManicTime consists of two processes - ManicTime.exe (tracker) and ManicTimeClient.exe (User interface). If this is checked, when you close the main window, ManicTimeClient.exe will keep on running. This will consume more memory, but it will also show up more quickly when you click on ManicTime icon, since it is already running in the background.
If you want to conserve memory, uncheck it. This will unload ManicTimeClient.exe every time you close it, releasing any memory it was using, but it will start up slower.

Always run minimized - when checked, only ManicTime tracker will start, but the main window will not pop up

Start when Windows starts - when checked, ManicTime will be started when Windows starts

Automatically check for updates - ManicTime checks our server for updates once a day. To disable this behavior uncheck this option.

Enable ManicTime process monitor - We try to do everything we can to keep ManicTime from crashing. But since it is used on a lot of machines, with different hardware and software, it does crash from time to time. If you enable this setting, a new process(ManicTimeProcessMonitor.exe) will be started when ManicTime starts. ManicTimeProcessMonitor.exe will monitor ManicTime and if it crashes, it will automatically start it again.  

Stop stopwatch when application exits - stopwatch can continue running even after you stop ManicTime.  

First day of week - select with which day the week starts

Shift day start by (hours) - set the hour with which the day starts More about this