Delay between timers possible?
If both timers are run from the same clock source (a divider doesn't matter) and you do not stop and restart those timers manually, there will be no delay between them since the timers work synchronously (they are bound to a clock). Yet, your clock will probably be skewed over time (but both timers will be skewed by the same amount), so you might be better off with a dedicated RTC.

You could then connect the seconds interrupt of your RTC to an external interrupt input and rely on this source. 

I am not quite sure why you would need two timers for this task as this is something which can easily be accomplished by a single timer if you do not care for a few non-accumulating clock cycles delay (which are used in your main loop).