What do you do if your saddle on your guitar is pushed all the way back and needs to be pushed more to be correctly intonated?
Intonation compensation is a common set up procedure.
However, different bridges can require different treatment.
Electrics:some bridges like the classic fender or the Gibson
"tune o' matic" can be easily worked since the saddles sits on
even Floyd rose bridges have Allen screws.
acoustic/classic bridges - you need to make sure that the saddle
fits the slot and is nicely smoothed to be correct - not always an
easy task for the novice. if the saddle is to thin and wiggle you
can use a piece of thin carton to tighten it in the slot.
in any case use a tuner and make sure that the twelve fret gives
you an accurate octave.
needles to say your nut should be accurate as well - by
functioning as a zero fret.