If this were the coffee house Mike, I would say I prefer yellowfish tuner. Damn ! I said it

Mike, my guess is the only thing you're missing is time doing it.

I believe most guitarist start by playing unison notes at the 5th fret after
tuning one string to a source. Then they try harmonic's and wind up in a loop
if the guitar hasn't had the intonation set. Meaning it will be kinda in tune at the low
end of the fretboard and out higher up. Or it will tune higher and then it's out on the low.

I can understand guitarist taking the easy out with a tuner and just wanting to play.
I don't agree with it but understand.

It's a good thing to be able to rake across the strings and dial them in within a few cents.
You're body will learn the vibrations too.
I sure recommend making "tuning" part of your practice time. 
If you do..a tip...always tune up to the pitch. If you pass it, back off and come back up to it. ( I imagine you already know this)

Regards,
Michael