Well, just speaking for classical guitar, if the e,b,e is suggested by the arranger or composer to be played in a specific place a circle with the string number would be under the notated e which would imply the other notes are taken at that position too. So in this case, it would be 5 in the circle to indicate the a string. This is quite typical of the instrument I grew up with. I'll say usually as one phrase may be repeated, it is often contrasted for a different color by playing it somewhere else on the fingerboard. Using a circle for bass in this case then, a 3 in a circle to indicate the lowest note e is to be played at the 7th fret of the a string would be the clarifier.