For what it's worth, I only use the stone tuner, and I only ever use it to tune my open high E, then I tune the guitar by ear to itself using fourths and fifths with high gain to accentuate the beats in dissonance. I recheck the high E as I go along. If the tuner that shows up in regular editing pages shows in off and I can hear a problem, I open the strobe to check. I have an FC12, but I still just use the strobe on the front panel.
I'm crazy about intonation, and I've had two Buzz Feiten system guitars (a holy grail Washburn USA P3 and now a Washburn Parallaxe Trevor Rabin), and I find the system to help immensely; too bad it never caught on more.
This is a very personal thing, but I use my ear for intonation too. I use fretted notes at the 5th and 17th on the high E and just tweak until they sound right, then I play 4ths and 5ths between the B and high E, adjusting the B until those intervals harmonize in tune as far up the neck as practical. I continue to each lower pitch adjacent string with 4ths and fifths on high gain until I hit the low E.
I've always wanted to try a True Temperament neck to get much closer with M3rds and M3rds, but I like my method.
Since I constantly reference the high E to a tuner, then I check the rest of the strings against it in context, my guitar sounds very in tune. I generally play an open E power chord: low E, 2nd fret of the A and D, mute the G, open B and high E, then an open G power chord: 3rd fret of the low E, open D and G, to check that the G is in the ballpark, then I fine tune the G by playing its most troublesome spots: open G against 1st fret of the B, and 2nd fret of the G against 5th fret of the B. Again, I double check that high E constantly against the tuner as I do this.
This tension between the two trouble spots on the G really help smooth it out to being as strongly in tune as a bastard string like that can be. It oscillates in a less stable way than any other string, since it's so thick for being unwound. I find that the open G / 1st fret of B 4th wants a the G to be sharper than the 2nd fret of G / 5th fret of B 5th interval, so I go between that 4th and 5th quite a bit, tuning the G up with the 4th and down with with 5th until it balances as well as possibly between the two, playing hard and soft. And to clarify, when I say "tune down," I move the tuning peg below the target pitch, stretch the string, then tune up to the desired pitch from there, so technically I always tune up to pitch no matter what.
When I play with my Floyd, that's a different ballgame, but still I just tune to myself by ear, using the strobe to set a reference for the high E only.
All of musical tuning is based on compromise and trying to maximize harmony between the most mathematically stable internal intervals in the overtone series, so you're strongest are always the octave and fifth. Interesting to consider that in the Renaissance the perfect fourth was considered dissonant! The main thing is, as with all considerations in audio and music, how it strikes an audience. A more in tune guitar always sounds more powerful and professional, and any duet, group or ensemble sounds stronger when they're aware of and in control of how they are handling their harmonic relationships between the members. This is one reason I'm an insane dickhead about programming the pitch block for my myself by ear, getting it technicality sharp or flat as far as the computer is concerned, until it actual sounds pleasing, and when I use diatonic harmonies I'll check, for the context of a part, whether equal or just temperament works better for the intervals I'm landing on. This is a huge power within the Fractal products.
