I think its safe to say that whoever originally found the wheel didn't just happen upon it one day while randomly digging a 100 foot hole in the middle of the jungle. There had to have been some sort of sign; a clue leading them there.
What was the clue you ask? The rope! If you remember in "This Place is Death" when Sawyer feeding the rope to lower John in the bucket down the well that a time-flash occurs burying John deep below in cave. Sawyer, on the other end, is above ground grasping the rope leading directly into the ground because The Well had not been built yet. However the rope of the future Well had traveled with Sawyer back in time and was subsequently LEFT THERE before Sawyer and the others flashed onto 1974.
So if whatever happens, happened then that's what's always happened. Sawyer always time-traveled with the rope and left it in the ground before The Well was made.
It is my belief that if we ever see The Well being dug that it will be because somebody found the rope sticking out the ground one day, thought it strange and because they had never seen it before and when they started to try and dig it out. But the rope just kept going further and further down, other people will join in with the effort and then eventually they reach the cave with The Wheel.
But after The Well had been in use, it was put OUT OF USE. We see this in "LaFleur" when Sawyer and the others have their last time-flash to 1974. Sawyer goes to jump down the Well but is he finds that it has been covered up with dirt and rocks. Now this odd artifact is noticed by DHARMA and they start their own Well, The Orchid. It would be sort of poetic to see that two different civilizations on The Island stumble upon this Cave and this Wheel by discovering these odd artifacts leading them to dig to it; the buried rope leads to the well and the buried well leads to the Orchid.
I know what you're asking... "But how did the Wheel get there?" The origin of the Wheel can give you a bit of a headache but this theory was meant to be more of theory about why the Well was built and how The Wheel was discovered.