Reminds me of this a bit, a copy of which I've had hanging since forever on my cube wall at work:
I don't think we have a "direct" way to know, it usually just comes down to functioning on a holistic level. When something continues to function in a way that satisfies intent and need, we tend to accept it as at least sufficient if not ideal; when things break down and cannot function, we seek a solution.
For example, when our car doesn't do what we've come to expect it to do (e.g., start when we turn the key), we don't necessarily know what is wrong, but we take it to a mechanic. Sometimes a problem is common enough that it can become expected at a certain age in the car's life, or whatever -- so it gets integrated into our body of knowledge. But basically we can't perceive the answer from our vantage point, we just know there is a problem because something has changed and the car is not functioning "as cars are supposed to."
This typically works for other things as well... either something loses its internal coherency or functions contradictory to our current understanding, and THAT is when we think there is a problem and try to investigate further.
But what of "Matrix" thought, where everything seems to be functioning, inconsistencies can be explained away somehow (or do not break the perceptive framework irrevocably). How would we know? ANother question, though, could also be, why would we care?
If the world is actually on the back of a giant tortoise, and that knowledge has no measurable impact on our lives and/or doesn't change anything -- if "Functional" perceivable reality is what governs our experienced lives -- then we can ask the question of, "Does the 'truth' here really matter in terms of how we live and understand our world?" or what about the obsession over something that could never be tested or proved, that meanwhile distracts from functioning well in your current life...? Does it matter?
That is an interesting question to me.