Would it work to put each "clock" in it's own floating document window? (Windows of this type are not modal so you can continue to edit data in another window, but do "float" in front of other windows and thus won't disappear behind behind other windows.)
With a window for each, you could use InstallOnTimerScript on both windows to set up a separate timer on each. Getting smooth updates in all windows may not be practical, however. You'd need to test it and see.
I am not sure about the Install OnTimerSchript, never used this script, is there sample somewhere?
You can look it up in help.
This step selects a script to be performed every x seconds. The seconds are specified in the parameter so you select a script and specify the interval in seconds. You can do this once to set up a timer from the context of any one window--hence my suggestion for two windows. The script you select would add 1 to a field or variable displayed in that window and you'll probably need to refresh the object after each update. (give the field or merge variable an object name and use refresh object to update its display after each time the value is changed).
The specified script will continue to be performed at intervals until you either close its window or you "cancel" the timer. To cancel the timer, use install OnTimeScript again but with no parameters specified.
when you read up on InstallOnTimerScript, pay special attention to how they act in multiple windows.
Also, if your timers need to be time-accurate, then you should probably use the timed script to update your display fields using a calculation based on GetAsNumber(Get(CurrentTime) - $startTime)