There's 100 ways to skin a rabbit. For me, AT FIRST I use a "note finder" you know the kind you blow into? However, I ONLY blow into E (first, thinnest string) note and then adjust all the other strings by that one. If E is perfectly in tune all the rest will follow. THEN I use the electronic tuner to refine the tone.
But remember, when you adjust E string the neck goes foreward so by the time you get to E (thickest string) then E thinnest string will be off slightly so you have to go back and tune each one until the neck is totally set.
Dunno if that helps at all but that's my 3 cents.