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While there's no precise explanation as to what the hidden message "Search For The BlindEye" means, I believe I have figured out what it ties in to in the show.
Looking at the symbol on Grunkle Stan's fez, both the original design and the modified design, they both depict a basic shape of a sphere with an open space to the left, and a flat attachment to the right.
If those deisgns are a cross-view of a three dimensional image, the entire image would be that of a sphere, which would look a lot like an eyeball.
My theory is that the "Blindeye" is the basis for this design, and the fact that it is on Grunkle Stan's fez means that he is either part of a society that has ties to whatever the "Blindeye" is, or the fez itself holds something mysterious.
Turning a blind eye literally means to ignore something. I think that the "blindeyes" are people in Gravity Falls who know of the town's strange goings-on but choose to ignore it for some (probably sinister) reason. So far, I think they include Stan, Soos, and Mckgucket.