How do you get the Clock to show elapsed time for the full flight and not just for 60 minutes.  I read the manual but even so can't seem to get it to work.  

You've probably pressed the the CHR button. The elapsed timer switch is bottom left of the clock.

Yes, that's it.  Are you able to flip between the two or is it one or the other?

You can use both. The ET will run in the background if you use CHR.