Normally there's no good reason to make sure your clearo runs dry, unless it's time to dry burn it....however, you will notice that as you use it, the juice will darken over time. It does this for two reasons. 1st, juice reacts to sunlight and will just darken over time. This IMO, does not change the flavor of your juice. 2nd, What I call "backwash" is when juice is fed to the coil and then released back into the tank after you stop vaping. This will affect the flavor IME, and will only get worse over time. Myself, I usually will top off my tanks 3 or 4 times before I vape it down as far as I can, then clean the tank and coil.
As for the batteries you use? The button will flash when the level has reached a certain point, which I believe is 3.2volts? Some will go as low as 2.7, but I don't like that low a charge as that is almost to the point where damage can occur. Todays battery technology is different from old style NIMH where they had a battery memory. That is to say, that if you ran it down to a certain point several times and then charge it, it will keep the level for ever. Hard to explain, but it really doesn't matter any more anyways.