I prefer to notate the pitch you hear, with a little 'o' above the note head... it makes sense to me because a score usually gives instructions about what the music should sound like, and usually leaves it up to the reader to decide things like where on the fingerboard you should play
and given that the same harmonic pitch can be played at more than one place on the fingerboard, I think this is a justifiable thing to do
if you're writing TAB or a notation/TAB hybrid, then I can see how 'instructions on where your fingers go' type notation would make sense, but i'm not into TAB
I prefer to use leger lines than treble clef or octave markings... I think bass players generally prefer it up to about 4 lines