Certainty and Skeptical Investigation

I know Buddhism promotes skeptical investigation, and finding things out with a personal conviction about them, i.e. not believing the Buddha on hearsay but rigorous examination. I wonder: how is such a certainty achieved? I would think the combination of shamatha and vipassana is the answer, but I wonder what EXACTLY is the closest determinant of a feeling of certainty, whether sensory (seeing something and *feeling* quite certain of the perception) or cognitive (*feeling* certain of some analytical reasoning). Personally, I feel like I often achieve a feeling of certainty, but it usually fades into doubts and alternate hypothesis. I can't seem to generate a sturdy sense of truth. I appreciate any answer to this question. Thank you.