don't worry, those aren't dumb questions
 
in theory, if the end key was different than the start key.. then when you're mixing out, you'd want to match the end key with the start key of the next track (RE2 does this automatically for you if you set the current song and click "key search").  really, its about matching the key of the song at the instant you're playing the songs...  and keys can very in some songs, but allowing a separate start/end key seemed to be the best way to handle that problem (start/end being where you'd normally mix in/out of a song)
 
as far as detection methods, from file would be best (with the detection quality turned up highest).  from live input might skip some frames if the cpu gets behind... but for the live audio input to be the same, you'd have to start it at the beginning of the song and play it to the end.  every time you stop/restart the live input it resets the internal counters, but otherwise the key that reads is the average key from the time you started it to the current point in time

if you don't hear the sound in eartraining or piano, go under options->audio and try changing the midi output ... hope that helps!