This is a massively broad question, that basically asks the global question of how we should do epistemology.
I can offer the answer that I have found in my exploration of philosophy.
There are, broadly, three ways we can acquire knowledge:
a) logical deduction
b) direct intuition
c) indirect inference
a) Logical deduction, is basically the method pursued by the analytic approach to philosophy. Identify logical necessities, and infer their reality. In the Western philosophic tradition, Thomas Aquinas exemplifies an analytic approach to philosophy and epistemology.
b) direct intuition is appealed to by disparate philosophic traditions. Intuitions are appealed to by Thomists (that logic is intuitively true, for instance), by materialists (direct realism holds that we just KNOW the physical world is real and as we experience it), by idealist phenomenologists (we KNOW the phenomena we experience, and the reality of that phenomena is unquestionable), and by spiritual mystics (the insights of the Buddha are of the TRUE REALITY).
c) Indirect inference assumes that we do NOT have direct and certain knowledge of the world, and we must make uncertain inferences about it. The methodology that we have developed to do this is empiricism, which we have tuned and refined to use in science. Karl Popper is our best articulator of the science process, which is to: explore a subject, develop speculations, do further guided explorations and refine/tune our speculations, develop hypotheses then test them, toss or refine hypotheses based on test results, repeat and tune until hypotheses pass multiple tests and we can trust them to likely be valid.
Socrates taught us to question the assumptions behind the boxes we think within. One can apply the test/refute process of c), to the claims of the other two methods of knowledge. Relative to "Direct realism" -- modern physics claims that "reality" is nothing like our familiar world, and instead consists of elementary particles, probability fields, etc. This idea is called "scientific realism", and holds that our actual reality is very different from our assumptions about reality.
This approach of empirical testing of the trustworthiness of our intuitions has been applied to perception as well. We know that we experience delusions, false memories, and sometimes invented memories. A good summary of the "anti-trustworthiness of perception" evidence can be found in David Eagleman's book Incognito: https://www.goodreads.com/book/show/9827912-incognito
And the trustworthiness of our intuitive "logic" was first challenged when we discovered that Euclidean Geometry was NOT "intuitively true", and did not actually even apply to this world! Subsequently, logicians have discovered that not only can infinite different math structures be constructed, but so can infinite logics! https://www.cambridge.org/core/journals/think/article/abs/guide-to-logical-pluralism-for-nonlogicians/EDFDFA1C9EB65DB71848DABD6B12D877
What these tests of our intuitions show, is that our intuitions can be fooled. They are not reliable. As can our "reasoning". See https://www.goodreads.com/book/show/11468377-thinking-fast-and-slow.
What we are left with, then, is really only method c). Indirect inference, which applies to both our intuitions and our reasoning.
There are major consequences to our understanding of reality from only having c) available to us.
There is no certainty we can ever have. We can NEVER know if we have "got it right"
All knowledge is judgment based. We interpret our perceptions and intuitions. There is no certain or reliable formula to do this. The best method we have come up with, is to reach consensus with other humans of good judgement. And there is no certain formula for "good judgement" either...
Subjectivity, judgement, consensus, skepticism, and uncertainty are therefore intrinsic to how we have to live in this world.
