I am guessing the Timer1.value sets the value of the first time in Seconds?
Yes, the event hander for Timer1 (OnTimer1Tick) will be called 5 seconds after Timer1 is enabled
Does it run through the setup each time? I guess once you define the value in the setup, it checks if it's actually equal to that.
Once the value is set it will be maintained until it is explicitly set to something else. The timer will actually continue to trigger every 5 seconds unless it is disabled, which is why it is disabled for your applicaiton when it matures, and re-enabled when a trigger arrives on the serial port.
Finally, whatever the time it might be, I also need to run a 2 digit LED display. I already checked some inbuilt libraries, but I had a hard time understanding them. I just need it do a countdown from 30 seconds. Thus every second it counts, I need it change the display to 30, 29... and reset it back to 30 once it's matured.
I would implement this using a timer with a value of 1 second. Each time the event handler is called I would decrement a counter initially set to 30 by 1. You could display this number on the lcd and turn the motor off when it gets to 0.
But, if this is the functionality you want, it may just be easier to do it using the millis counter, as per Mikes proposal.
Also, wouldn't the delay function cause the whole code to stop for a the defined time?
Calling Clock.Delay() blocks the foreground sketch for the given number of millis (one millisecond per loop in the example sketch) but the underlying code in the Clock.delay function is constantly checking the timer states to see if a timer has matured.
My suggestion if you have only a single delay going on at one time is to try Mikes approach first. But I will get you the code if you are comfortable modifying your copy of wiring.c